-------------------------------------------------------------------------------
--                                                                           --
--                           Automation Script File                          --
--                Delta NMR Processing and Control Interface                 --
--                                                                           --
--                    Copyright (c) 2017 JEOL RESONANCE, Inc.                --
--                           All Rights Reserved                             --
--                                                                           --
-------------------------------------------------------------------------------
C:\Users\delta\Documents\JEOL\Delta 5.3\automation
-------------------------------------------------------------------------------
-- IMPORTANT NOTES
-------------------------------------------------------------------------------
-- Remember that when assigning to the x_sweep parameter from another data file
-- (such as a scout scan) that we should obtain the 'x_sweep_clipped' parameter
-- value which will give the corrected x_sweep value that we expect.  This is
-- because digital filtering modifies the x_sweep value prior to acquisition.
-------------------------------------------------------------------------------

AUTOMATION VERSION 2;

PURPOSE "A collection of Methods for use with Delta v 5.3.x and higher.";

INCLUDE "Utilities" TO DOMAIN util;

ENUM Spinlock_field IS ("2[kHz]", "3[kHz]", "4[kHz]", "5[kHz]", "6[kHz]", "7[kHz]", "8[kHz]");

NUMBER Gain_Range IS INTEGER FROM 0 TO 102 STEP 2 WITH NO UNIT;

ENUM DOMS IS NAMESPACE CAPITALIZE KEYS "gamma" IGNORE ("nodraw");

NUMBER Sel_angle IS LIST (45, 90, 135) WITH UNIT [deg];

NUMBER SamplingPoints IS LIST (64, 128, 256, 512);

NUMBER SamplingDensity IS LIST (6.25, 12.5, 25, 50, 62.5, 75);

ENUM LinearNus IS ("Linear", "Nus");

-------------------------------------------------------------------------------

METHOD " 1. 1H" IS

    PURPOSE "Routine Proton single pulse experiment";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             120[s];

           VAR calculate_proton_90 : BOOLEAN    = FALSE;--,   HELP "Calculate 90 degee pulse?";
           VAR force_tune          : BOOLEAN    = FALSE;--,   DEPENDS ON calculate_proton_90 EVALUATE (calculate_proton_90 ? TRUE : FALSE),
--                                                           HELP "Retune RF coil(s)";
           VAR dual_tuned          : BOOLEAN    = FALSE;--,   HELP "Dual tuning for HFX probes";
           VAR autogain            : BOOLEAN    = TRUE;--,    HELP "Optimize gain value automatically";
           VAR receiver_gain       : Gain_Range = 0;--,       DEPENDS ON autogain EVALUATE (autogain ? 0 : 46);
    EXPOSE VAR scans               : NUMBER     = 32,      HELP "Number of scans to perform";
           VAR dummy_scans         : NUMBER     = 0;--,       HELP "Dummy scans";
           VAR tip_angle           : NUMBER     = 45[deg];--, HELP "Tip angle";
    EXPOSE VAR x_offset            : NUMBER     = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR x_sweep             : NUMBER     = 15[ppm], HELP "Sweep width";
           VAR data_points         : NUMBER     = 32768;--,   HELP "Number of data points";
    EXPOSE VAR relaxation_delay    : NUMBER     = 4[s],    HELP "Pre-pulse delay";

    VAR comment    : TEXT = SAMPLE "comment";
    VAR obs_domain : TEXT = "Proton";
    VAR oneh_coil  : TEXT = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = receiver_gain;
            relaxation_delay = relaxation_delay;
            scans            = scans;
            x_angle          = tip_angle;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = data_points;
            x_prescans       = dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

END METHOD " 1. 1H";

-------------------------------------------------------------------------------

METHOD " 2. 13C" IS

    PURPOSE "Routine Carbon single pulse experiment";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION carbon +
              120[s];

    		VAR calculate_carbon_90 : BOOLEAN    = FALSE;--,    HELP "Calculate 90 degee pulse?";
    		VAR force_tune          : BOOLEAN    = FALSE;--,    DEPENDS ON calculate_carbon_90 EVALUATE (calculate_carbon_90 ? TRUE : FALSE);
           VAR dual_tuned          : BOOLEAN    = FALSE;--,    HELP "Dual tuning for HFX probes";
           VAR autogain            : BOOLEAN    = TRUE;--,     HELP "Optimize gain value automatically";
           VAR receiver_gain       : Gain_Range = 0;--,        DEPENDS ON autogain EVALUATE (autogain ? 0 : 46);
    EXPOSE VAR scans               : NUMBER     = 256,      HELP "Number of scans to perform";
           VAR dummy_scans         : NUMBER     = 4;--,        HELP "Dummy scans";
           VAR tip_angle           : NUMBER     = 30[deg];--,  HELP "Tip angle";
           VAR sn_ratio            : NUMBER     = 0;--,        HELP "Stop when s/n is achieved, 0 = skip test";
    EXPOSE VAR x_offset            : NUMBER     = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR x_sweep             : NUMBER     = 250[ppm], HELP "Sweep width";
           VAR data_points         : NUMBER     = 32768;
    EXPOSE VAR relaxation_delay    : NUMBER     = 2[s],     HELP "Pre-pulse delay";

    VAR comment           : TEXT = SAMPLE "comment";
    VAR obs_domain        : DOMS = "Carbon13";
    VAR irr_domain        : DOMS = "Proton";
    VAR oneh_coil         : TEXT = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET 5[ppm];

    INVOKE util.Set_1H_90_Params( before_tune_idler );

    INVOKE util.gs();

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_carbon_90 = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_carbon_90, autogain, receiver_gain, 90[deg], dual_tuned );

    IF calculate_carbon_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF carbon_rg /= NULL THEN
        SET receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = relaxation_delay;
            scans            = scans;
            recvr_gain       = receiver_gain;
            sn_ratio         = sn_ratio;
            x_angle          = tip_angle;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = data_points;
            x_prescans       = dummy_scans;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE carbon;

    PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon SAVE AS "$(SAMPLE)_CARBON_FT";

    PRESENTATION carbon_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_CARBON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;

END METHOD " 2. 13C";

-------------------------------------------------------------------------------
METHOD " 3. 1H & COSY" IS

    PURPOSE "Proton-Proton correlation spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +

             120[s];

    		VAR calculate_proton_90     : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR autogain                : BOOLEAN         = TRUE;
    		VAR receiver_gain           : Gain_Range      = 0;

    EXPOSE VAR proton_scans            : NUMBER          = 16,      HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm], HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],    HELP "Pre-pulse delay for Proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,       HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],  HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,     HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            scans            = proton_scans;
            recvr_gain       = receiver_gain;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            relaxation_delay = proton_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

END METHOD " 3. 1H & COSY";

-------------------------------------------------------------------------------

METHOD " 4. 1H & 13C" IS

    PURPOSE "Proton and Carbon";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             carbon +
             120[s];

    		VAR calculate_90s           : BOOLEAN    = FALSE;
    		VAR force_tune              : BOOLEAN    = FALSE;
    		VAR dual_tuned              : BOOLEAN    = FALSE;

    		VAR proton_autogain         : BOOLEAN    = TRUE;
    		VAR proton_receiver_gain    : Gain_Range = 0;
    EXPOSE VAR proton_scans            : NUMBER     = 16,       HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER     = 0;
    		VAR proton_tip_angle        : NUMBER     = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER     = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER     = 15[ppm],  HELP "Sweep width";
    		VAR proton_data_points      : NUMBER     = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER     = 4[s],     HELP "Pre-pulse delay for proton experiment";

    		VAR carbon_autogain         : BOOLEAN    = TRUE;
    		VAR carbon_receiver_gain    : Gain_Range = 0;
    EXPOSE VAR carbon_scans            : NUMBER     = 256,      HELP "Number of scans to perform";
    		VAR carbon_dummy_scans      : NUMBER     = 4;
    		VAR carbon_tip_angle        : NUMBER     = 30[deg];
    		VAR carbon_sn_ratio         : NUMBER     = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER     = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR carbon_x_sweep          : NUMBER     = 250[ppm], HELP "Sweep width";
    		VAR carbon_data_points      : NUMBER     = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER     = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    VAR comment           : TEXT = SAMPLE "comment";
    VAR obs_domain        : DOMS = "Carbon13";
    VAR irr_domain        : DOMS = "Proton";
    VAR oneh_coil         : TEXT = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    CONCEAL EXPERIMENT carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = carbon_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = carbon_relaxation_delay;
            scans            = carbon_scans;
            recvr_gain       = carbon_receiver_gain;
            sn_ratio         = carbon_sn_ratio;
            x_angle          = carbon_tip_angle;
            x_points         = carbon_data_points;
            x_prescans       = carbon_dummy_scans;
            x_offset         = carbon_x_offset;
            x_sweep          = carbon_x_sweep;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE carbon;

    PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon SAVE AS "$(SAMPLE)_CARBON_FT";

    PRESENTATION carbon_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_CARBON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;

END METHOD " 4. 1H & 13C";

-------------------------------------------------------------------------------

METHOD " 5. 1H, 13C & COSY" IS

    PURPOSE "Proton, Carbon, DQF COSY";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             carbon +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +
             120[s];

    		VAR calculate_90s           : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR proton_autogain         : BOOLEAN         = TRUE;
    		VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay for proton experiment";

    		VAR carbon_autogain         : BOOLEAN         = TRUE;
    		VAR carbon_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR carbon_scans            : NUMBER          = 256,      HELP "Number of scans to perform";
    		VAR carbon_dummy_scans      : NUMBER          = 4;
    		VAR carbon_tip_angle        : NUMBER          = 30[deg];
    		VAR carbon_sn_ratio         : NUMBER          = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER          = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 250[ppm], HELP "Sweep width";
    		VAR carbon_data_points      : NUMBER          = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER          = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_clip            : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,        HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    VAR comment           : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base  : NUMBER = 1;
    VAR obs_domain        : DOMS   = "Carbon13";
    VAR irr_domain        : DOMS   = "Proton";
    VAR oneh_coil         : TEXT   = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";
    VAR xoffset           : NUMBER = proton_x_offset;
    VAR xsweep            : NUMBER = proton_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    CONCEAL EXPERIMENT carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = carbon_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = carbon_relaxation_delay;
            scans            = carbon_scans;
            recvr_gain       = carbon_receiver_gain;
            sn_ratio         = carbon_sn_ratio;
            x_angle          = carbon_tip_angle;
            x_points         = carbon_data_points;
            x_prescans       = carbon_dummy_scans;
            x_offset         = carbon_x_offset;
            x_sweep          = carbon_x_sweep;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE carbon;

    PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon SAVE AS "$(SAMPLE)_CARBON_FT";

    PRESENTATION carbon_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_CARBON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, xoffset, xsweep );
        INFORM "x_offset set to $(xoffset)";
        INFORM "x_sweep set to $(xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = xoffset;
            x_sweep          = xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

END METHOD " 5. 1H, 13C & COSY";

-------------------------------------------------------------------------------

METHOD " 6. 1H, 13C, COSY & edHSQC" IS

    PURPOSE "Proton, Carbon, DQF COSY, Edited HSQC";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             carbon +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * hsqc +
             
             120[s];

    		VAR calculate_90s           : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR proton_autogain         : BOOLEAN         = TRUE;
    		VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay for proton experiment";

    		VAR carbon_autogain         : BOOLEAN         = TRUE;
    		VAR carbon_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR carbon_scans            : NUMBER          = 256,      HELP "Number of scans to perform";
    		VAR carbon_dummy_scans      : NUMBER          = 4;
    		VAR carbon_tip_angle        : NUMBER          = 30[deg];
    		VAR carbon_sn_ratio         : NUMBER          = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER          = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 250[ppm], HELP "Sweep width";
    		VAR carbon_data_points      : NUMBER          = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER          = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";    

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,        HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;



    		VAR perform_carbon_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR hsqc_scans              : NUMBER          = 2,        HELP " Number of scans for HSQC experiment";
    EXPOSE VAR hsqc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HSQC experiment";
    		VAR hsqc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hsqc_y_points           : SamplingPoints  = 128,      HELP "t1 increments";
    		VAR hsqc_sampling_density   : SamplingDensity = 25;

    VAR comment           : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base  : NUMBER = 1;
    VAR obs_domain        : DOMS   = "Carbon13";
    VAR irr_domain        : DOMS   = "Proton";
    VAR oneh_coil         : TEXT   = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";
    VAR proton_xoffset    : NUMBER = proton_x_offset;
    VAR proton_xsweep     : NUMBER = proton_x_sweep;
    VAR carbon_xoffset    : NUMBER = carbon_x_offset;
    VAR carbon_xsweep     : NUMBER = carbon_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    CONCEAL EXPERIMENT carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = carbon_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = carbon_relaxation_delay;
            scans            = carbon_scans;
            recvr_gain       = carbon_receiver_gain;
            sn_ratio         = carbon_sn_ratio;
            x_angle          = carbon_tip_angle;
            x_points         = carbon_data_points;
            x_prescans       = carbon_dummy_scans;
            x_offset         = carbon_x_offset;
            x_sweep          = carbon_x_sweep;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE carbon;

    PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon SAVE AS "$(SAMPLE)_CARBON_FT";

    PRESENTATION carbon_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_CARBON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF perform_carbon_clip THEN
        INVOKE util.Handle_Clipping( processed_carbon, carbon_xoffset, carbon_xsweep );
        INFORM "Carbon y_offset set to $(carbon_xoffset)";
        INFORM "Carbon y_sweep set to $(carbon_xsweep)";
    END IF;

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hsqc_y_points, hsqc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_inverse_pn.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_inverse_pn_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HSQC IS
        SAVE AS "$(SAMPLE)_HSQC$(fname_ext)";
        COLLECT "hsqc";
        SET * = params;
        SET scans            = hsqc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_xoffset;
            y_sweep          = carbon_xsweep;
            x_points         = hsqc_x_points;
            y_points         = hsqc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hsqc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HSQC;

    VAR processed_hsqc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HSQC WITH "2d_inverse_pn.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC_FT";
        SET processed_hsqc = processed_hsqc_temp;
    ELSE
        PROCESS HSQC WITH "2d_inverse_pn_nus.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC$(fname_ext)_FT";
        SET processed_hsqc = processed_hsqc_temp;
    END IF;

    PRESENTATION hsqc_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_hsqc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HSQC$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hsqc AND hsqc_pdf;

END METHOD " 6. 1H, 13C, COSY & edHSQC";

-------------------------------------------------------------------------------

METHOD " 7. 1H, 13C, COSY, edHSQC, HMBC" IS

    PURPOSE "Proton, Carbon, DQF COSY, Edited HSQC, HMBC";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             carbon +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * hsqc +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * hmbc +
             
             120[s];

    		VAR calculate_90s           : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;

    		VAR proton_autogain         : BOOLEAN         = TRUE;
    		VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay for proton experiment";

    		VAR carbon_autogain         : BOOLEAN         = TRUE;
    		VAR carbon_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR carbon_scans            : NUMBER          = 256,      HELP "Number of scans to perform";
    		VAR carbon_dummy_scans      : NUMBER          = 4;
    		VAR carbon_tip_angle        : NUMBER          = 30[deg];
    		VAR carbon_sn_ratio         : NUMBER          = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER          = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 250[ppm], HELP "Sweep width";
    		VAR carbon_data_points      : NUMBER          = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER          = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,        HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    		VAR perform_carbon_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR hsqc_scans              : NUMBER          = 2,        HELP " Number of scans for HSQC experiment";
    EXPOSE VAR hsqc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HSQC experiment";
    		VAR hsqc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hsqc_y_points           : SamplingPoints  = 128,      HELP "t1 increments";
    		VAR hsqc_sampling_density   : SamplingDensity = 25;

    EXPOSE VAR hmbc_scans              : NUMBER          = 4;
    EXPOSE VAR hmbc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HMBC experiment";
    		VAR hmbc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hmbc_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR hmbc_sampling_density   : SamplingDensity = 25;

    VAR comment           : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base  : NUMBER = 1;
    VAR obs_domain        : DOMS   = "Carbon13";
    VAR irr_domain        : DOMS   = "Proton";
    VAR oneh_coil         : TEXT   = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";
    VAR proton_xoffset    : NUMBER = proton_x_offset;
    VAR proton_xsweep     : NUMBER = proton_x_sweep;
    VAR carbon_xoffset    : NUMBER = carbon_x_offset;
    VAR carbon_xsweep     : NUMBER = carbon_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;
    
    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    CONCEAL EXPERIMENT carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = carbon_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = carbon_relaxation_delay;
            scans            = carbon_scans;
            recvr_gain       = carbon_receiver_gain;
            sn_ratio         = carbon_sn_ratio;
            x_angle          = carbon_tip_angle;
            x_points         = carbon_data_points;
            x_prescans       = carbon_dummy_scans;
            x_offset         = carbon_x_offset;
            x_sweep          = carbon_x_sweep;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE carbon;

    PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon SAVE AS "$(SAMPLE)_CARBON_FT";

    PRESENTATION carbon_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_CARBON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF perform_carbon_clip THEN
        INVOKE util.Handle_Clipping( processed_carbon, carbon_xoffset, carbon_xsweep );
        INFORM "Carbon y_offset set to $(carbon_xoffset)";
        INFORM "Carbon y_sweep set to $(carbon_xsweep)";
    END IF;

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hsqc_y_points, hsqc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_inverse_pn.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_inverse_pn_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HSQC IS
        SAVE AS "$(SAMPLE)_HSQC$(fname_ext)";
        COLLECT "hsqc";
        SET * = params;
        SET scans            = hsqc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_xoffset;
            y_sweep          = carbon_xsweep;
            x_points         = hsqc_x_points;
            y_points         = hsqc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hsqc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HSQC;

    VAR processed_hsqc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HSQC WITH "2d_inverse_pn.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC_FT";
        SET processed_hsqc = processed_hsqc_temp;
    ELSE
        PROCESS HSQC WITH "2d_inverse_pn_nus.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC$(fname_ext)_FT";
        SET processed_hsqc = processed_hsqc_temp;
    END IF;

    PRESENTATION hsqc_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_hsqc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HSQC$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hsqc AND hsqc_pdf;

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF perform_carbon_clip THEN
        INVOKE util.Handle_Clipping( processed_carbon, carbon_xoffset, carbon_xsweep );
        INFORM "Carbon y_offset set to $(carbon_xoffset)";
        INFORM "Carbon y_sweep set to $(carbon_xsweep)";
    END IF;

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hmbc_y_points, hmbc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_hmbc_abs.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_hmbc_abs_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HMBC IS
        SAVE AS "$(SAMPLE)_HMBC$(fname_ext)";
        COLLECT "hmbc_pfg";
        SET * = params;
        SET scans            = hmbc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_xoffset;
            y_sweep          = carbon_xsweep;
            x_points         = hmbc_x_points;
            y_points         = hmbc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hmbc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HMBC;

    VAR processed_hmbc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HMBC WITH "2d_hmbc_abs.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC_FT";
        SET processed_hmbc = processed_hmbc_temp;
    ELSE
        PROCESS HMBC WITH "2d_hmbc_abs_nus.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC$(fname_ext)_FT";
        SET processed_hmbc = processed_hmbc_temp;
    END IF;

    PRESENTATION hmbc_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_hmbc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HMBC$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hmbc AND hmbc_pdf;

END METHOD " 7. 1H, 13C, COSY, edHSQC, HMBC";

-------------------------------------------------------------------------------

METHOD " 8. 1H, COSY, edHSQC, HMBC" IS

    PURPOSE "Proton, DQF COSY, Edited HSQC, HMBC";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * hsqc +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * hmbc +

             120[s];

    		VAR calculate_90s           : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;

    		VAR proton_autogain         : BOOLEAN         = TRUE;
    		VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay for proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,        HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    EXPOSE VAR carbon_x_offset         : NUMBER          = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 250[ppm], HELP "Sweep width";

    EXPOSE VAR hsqc_scans              : NUMBER          = 2,        HELP " Number of scans for HSQC experiment";
    EXPOSE VAR hsqc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HSQC experiment";
    		VAR hsqc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hsqc_y_points           : SamplingPoints  = 128,      HELP "t1 increments";
    		VAR hsqc_sampling_density   : SamplingDensity = 25;

    EXPOSE VAR hmbc_scans              : NUMBER          = 4,        HELP " Number of scans for HMBC experiment";
    EXPOSE VAR hmbc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HMBC experiment";
    		VAR hmbc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hmbc_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    		VAR hmbc_sampling_density   : SamplingDensity = 25;

    VAR comment           : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base  : NUMBER = 1;
    VAR obs_domain        : DOMS   = "Carbon13";
    VAR irr_domain        : DOMS   = "Proton";
    VAR oneh_coil         : TEXT   = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";
    VAR proton_xoffset    : NUMBER = proton_x_offset;
    VAR proton_xsweep     : NUMBER = proton_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, TRUE, 46, 90[deg], dual_tuned );

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;


    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hsqc_y_points, hsqc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_inverse_pn.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_inverse_pn_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HSQC IS
        SAVE AS "$(SAMPLE)_HSQC$(fname_ext)";
        COLLECT "hsqc";
        SET * = params;
        SET scans            = hsqc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_x_offset;
            y_sweep          = carbon_x_sweep;
            x_points         = hsqc_x_points;
            y_points         = hsqc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hsqc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HSQC;

    VAR processed_hsqc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HSQC WITH "2d_inverse_pn.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC_FT";
        SET processed_hsqc = processed_hsqc_temp;
    ELSE
        PROCESS HSQC WITH "2d_inverse_pn_nus.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC$(fname_ext)_FT";
        SET processed_hsqc = processed_hsqc_temp;
    END IF;

   VAR processed_carbon : DATA;
   SET processed_carbon = project( processed_hsqc);

    PRESENTATION hsqc_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_hsqc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HSQC$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hsqc AND hsqc_pdf;

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hmbc_y_points, hmbc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_hmbc_abs.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_hmbc_abs_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HMBC IS
        SAVE AS "$(SAMPLE)_HMBC$(fname_ext)";
        COLLECT "hmbc_pfg";
        SET * = params;
        SET scans            = hmbc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_x_offset;
            y_sweep          = carbon_x_sweep;
            x_points         = hmbc_x_points;
            y_points         = hmbc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hmbc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HMBC;

    VAR processed_hmbc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HMBC WITH "2d_hmbc_abs.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC_FT";
        SET processed_hmbc = processed_hmbc_temp;
    ELSE
        PROCESS HMBC WITH "2d_hmbc_abs_nus.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC$(fname_ext)_FT";
        SET processed_hmbc = processed_hmbc_temp;
    END IF;

    IF processed_carbon = NULL THEN
        SET processed_carbon = project( processed_hmbc);
    END IF;

    PRESENTATION hmbc_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_hmbc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HMBC$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hmbc AND hmbc_pdf;

END METHOD " 8. 1H, COSY, edHSQC, HMBC";

-------------------------------------------------------------------------------
-- METHOD " 8. Quantitative Carbon" IS
-------------------------------------------------------------------------------

METHOD " 9. DEPT" IS

    PURPOSE "Dept";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Dept +
             120[s];

    		VAR calculate_90s           : BOOLEAN    = FALSE;
    		VAR force_tune              : BOOLEAN    = FALSE;
    		VAR dual_tuned              : BOOLEAN    = FALSE;
    		VAR autogain                : BOOLEAN    = TRUE;
    		VAR receiver_gain           : Gain_Range = 0;
    EXPOSE VAR scans                   : NUMBER     = 256,      HELP "Number of scans to perform";
    		VAR dummy_scans             : NUMBER     = 4;
    EXPOSE	VAR selection_angle         : Sel_angle  = 135[deg];
    		VAR sn_ratio                : NUMBER     = 0;
    EXPOSE VAR x_offset                : NUMBER     = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR x_sweep                 : NUMBER     = 250[ppm], HELP "Sweep width";
    		VAR data_points             : NUMBER     = 32768;
    EXPOSE VAR relaxation_delay        : NUMBER     = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    VAR comment                        : TEXT   = SAMPLE "comment";
    VAR selection_angle_stripped_units : NUMBER = selection_angle`[];
    VAR obs_domain                     : DOMS   = "Carbon13";
    VAR irr_domain                     : DOMS   = "Proton";
    VAR oneh_coil                      : TEXT   = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET 5[ppm];

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, TRUE, 40, 90[deg], dual_tuned, before_tune_idler );

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, autogain, receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF carbon_rg /= NULL THEN
        SET receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT Dept IS
        SAVE AS "$(SAMPLE)_DEPT_$(selection_angle_stripped_units)";
        COLLECT "dept";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            recvr_gain       = receiver_gain;
            scans            = scans;
            selection_angle  = selection_angle;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            relaxation_delay = relaxation_delay;
            x_points         = data_points;
            x_prescans       = dummy_scans;
            x_pulse          = carbon_90;
            x_atn            = carbon_atn;
            irr_pulse        = proton_90;
            irr_atn          = proton_atn;
    END EXPERIMENT;

    VISUALIZE Dept;

    PROCESS dept WITH "carbon_autophase_p.list" TO processed_dept SAVE AS "$(SAMPLE)_DEPT$(selection_angle_stripped_units)_FT";

    PRESENTATION dept_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_dept
        TO JOB PRINTER AND FILE "$(SAMPLE)_DEPT_$(selection_angle_stripped_units).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH dept AND dept_pdf;

END METHOD " 9. DEPT";

-------------------------------------------------------------------------------

METHOD "10. Edited Dept" IS

    PURPOSE "Edited Dept";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Carbon +
             Dept_45 +
             Dept_90 +
             Dept_135 +
             
             120[s];

    		VAR calculate_90s    : BOOLEAN    = FALSE;
    		VAR force_tune       : BOOLEAN    = FALSE;
    		VAR dual_tuned       : BOOLEAN    = FALSE;
    		VAR autogain         : BOOLEAN    = TRUE;
    		VAR receiver_gain    : Gain_Range = 0;
    EXPOSE VAR scans            : NUMBER     = 256,      HELP "Number of scans to perform";
    		VAR dummy_scans      : NUMBER     = 4;
    		VAR sn_ratio         : NUMBER     = 0;
      	VAR tip_angle        : NUMBER     = 30[deg];
    EXPOSE VAR x_offset         : NUMBER     = 100[ppm], HELP "Center of spectrum";
    EXPOSE VAR x_sweep          : NUMBER     = 250[ppm], HELP "Sweep width";
           VAR data_points      : NUMBER     = 32768;
    EXPOSE VAR relaxation_delay : NUMBER     = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    VAR comment    : TEXT = SAMPLE "comment";
    VAR obs_domain : DOMS = "Carbon13";
    VAR irr_domain : DOMS = "Proton";
    VAR oneh_coil  : TEXT = "hf1";
    VAR before_tune_idler : TEXT   = NAMESPACE "system.probe_id_idler" ELSE "";

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET 5[ppm];

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, autogain, 40, 90[deg], dual_tuned, before_tune_idler );

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, autogain, receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF carbon_rg /= NULL THEN
        SET receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT Carbon IS
        SAVE AS "$(SAMPLE)_CARBON";
        COLLECT "carbon";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = relaxation_delay;
            scans            = scans;
            recvr_gain       = receiver_gain;
            sn_ratio         = sn_ratio;
            x_angle          = tip_angle;
            x_points         = data_points;
            x_prescans       = dummy_scans;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_90_width       = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_45 IS
        SAVE AS "$(SAMPLE)_DEPT45";
        COLLECT "dept_dec";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            recvr_gain       = carbon("recvr_gain");
            selection_angle  = 45[deg];
            x_offset         = carbon("x_offset");
            x_sweep          = carbon("x_sweep_clipped");
            relaxation_delay = relaxation_delay;
            irr_90           = proton_90;
            irr_atn          = proton_atn;
            x_pulse          = carbon_90;
            x_atn            = carbon_atn;
            scans            = carbon("scans")/2;
            CONSTRAIN scans MULTIPLE OF 8 INCREASE;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_90 IS
        SAVE AS "$(SAMPLE)_DEPT90";
        COLLECT "dept_dec";
        SET comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            recvr_gain       = dept_45("recvr_gain");
            scans            = dept_45("scans");
            selection_angle  = 90[deg];
            x_offset         = carbon("x_offset");
            x_sweep          = carbon("x_sweep_clipped");
            relaxation_delay = dept_45("relaxation_delay");
            irr_90           = proton_90;
            irr_atn          = proton_atn;
            x_pulse          = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_135 IS
        SAVE AS "$(SAMPLE)_DEPT135";
        COLLECT "dept_dec";
        SET comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            recvr_gain       = dept_45("recvr_gain");
            scans            = dept_45("scans");
            selection_angle  = 135[deg];
            x_offset         = carbon("x_offset");
            x_sweep          = carbon("x_sweep_clipped");
            relaxation_delay = dept_45("relaxation_delay");
            irr_90           = proton_90;
            irr_atn          = proton_atn;
            x_pulse          = carbon_90;
            x_atn            = carbon_atn;
    END EXPERIMENT;

    VAR tmp_carbon : DATA;
    VAR tmp_45     : DATA;
    SET tmp_45 = dept_45 - dept_135;

    VAR tmp_90  : DATA;
    VAR tmp_135 : DATA;
    SET tmp_135 = dept_45 + dept_135 - sqrt(2) * dept_90;

    SET tmp_carbon = clip( ppm( machinephase( fft( sexp( carbon, 2[Hz], 0[s] ) ) ) ), 1.2, FALSE );
    SET tmp_45     = ppm( machinephase( fft( sexp( tmp_45,  2[Hz], 0[s] ) ) ) );
    SET tmp_90     = ppm( machinephase( fft( sexp( dept_90, 2[Hz], 0[s] ) ) ) );
    SET tmp_135    = ppm( machinephase( fft( sexp( tmp_135, 2[Hz], 0[s] ) ) ) );

    PERCIVAL <<<
        -- Make a vector that can be linked to in PM that will allow the CH's to
        -- have the same y min and max based on the current data files
        function CREATE_MAX_FILE( in45 : FILE, in90 : FILE, in135 : FILE ) return FILE is
            var
                mm    : SET,
                max_y : NUMBER := -infinity,
                min_y : NUMBER := infinity,
                max_x : NUMBER := -infinity,
                min_x : NUMBER := infinity;

            for fl in {in45, in90, in135} loop
                mm := minmax( fl );
                -- Pick the max y value in the set of files(get the largest positive value)
                if mm(2) > max_y then
                    max_y := mm(2);
                end if;

                -- Pick the min y value in the set of files (get the largest negative value)
                if mm(1) < min_y then
                    min_y := mm(1);
                end if;

                mm := minmax {(bounds fl){3,1}, (bounds fl){4,1}};
                -- Pick the max x value in the set of files
                if mm(2) > max_x then
                    max_x := mm(2);
                end if;

                -- Pick the min x value in the set of files
                if mm(1) < min_x then
                    min_x := mm(1);
                end if;
            end loop;

            return vector {{max_x,max_y},{min_x,min_y}};
        end CREATE_MAX_FILE;
    >>>;

    VAR max_file : DATA;
    SET max_file = CALL create_max_file( tmp_45, tmp_90, tmp_135 );

    PROCESS tmp_carbon WITH "null.list" to tmp_carbon_ft SAVE AS "$(SAMPLE)_CARBON";
    PROCESS tmp_90 WITH "null.list" to tmp_90_ft SAVE AS "$(SAMPLE)_METHINES";
    PROCESS tmp_45 WITH "null.list" to tmp_45_ft SAVE AS "$(SAMPLE)_METHYLENES";
    PROCESS tmp_135 WITH "null.list" to tmp_135_ft SAVE AS "$(SAMPLE)_METHYLS";

    VISUALIZE tmp_135_ft WITH tmp_45_ft WITH tmp_90_ft WITH tmp_carbon_ft IN "data_slate";

    PRESENTATION edited_dept_pdf TEMPLATE "dept"
        WITH DATA tmp_carbon AND tmp_90 AND tmp_45 AND tmp_135 AND max_file
        TO JOB PRINTER AND FILE "$(SAMPLE)_EDITED_DEPT.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH Carbon AND Dept_45 AND Dept_90 AND Dept_135 AND edited_dept_pdf;

END METHOD "10. Edited Dept";

-------------------------------------------------------------------------------

METHOD "11. COSY" IS

    PURPOSE "Proton-Proton correlation spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * cosy +

             120[s];

    		VAR calculate_proton_90     : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR autogain                : BOOLEAN         = TRUE;
    		VAR receiver_gain           : Gain_Range      = 0;

    EXPOSE VAR proton_scans            : NUMBER          = 16,      HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm], HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],    HELP "Pre-pulse delay for Proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,       HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],  HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,     HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            scans            = proton_scans;
            recvr_gain       = receiver_gain;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            relaxation_delay = proton_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_COSY$(fname_ext)";
        COLLECT "cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH cosy AND cosy_pdf;

END METHOD "11. COSY";

-------------------------------------------------------------------------------

METHOD "12. DQF COSY" IS

    PURPOSE "Proton-Proton correlation spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](25) / 100)) * dqf_cosy +
             
			120[s];

    		VAR calculate_proton_90     : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR autogain                : BOOLEAN         = TRUE;
    		VAR receiver_gain           : Gain_Range      = 0;

    EXPOSE VAR proton_scans            : NUMBER          = 16,      HELP "Number of scans to perform";
    		VAR proton_dummy_scans      : NUMBER          = 0;
    		VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm], HELP "Sweep width";
    		VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],    HELP "Pre-pulse delay for Proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    		VAR perform_proton_clip     : BOOLEAN         = FALSE;
    EXPOSE VAR cosy_scans              : NUMBER          = 2,       HELP "Number of scans to perform";
    EXPOSE VAR cosy_relaxation_delay   : NUMBER          = 1.5[s],  HELP "Pre-pulse delay for Cosy experiemnt";
    		VAR cosy_x_points           : NUMBER          = 1024;
    EXPOSE VAR cosy_y_points           : SamplingPoints  = 256,     HELP "t1 increments";
    		VAR cosy_sampling_density   : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            scans            = proton_scans;
            recvr_gain       = receiver_gain;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            relaxation_delay = proton_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( cosy_y_points, cosy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "cosy.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_cosy_abs_nus_no_sym.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT DQF_COSY IS
        SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)";
        COLLECT "dqf_cosy_pfg";
        SET * = params;
        SET scans            = cosy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = cosy_x_points;
            y_points         = cosy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = cosy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE DQF_COSY;

    VAR processed_cosy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS DQF_COSY WITH "cosy.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_DQF_COSY_FT";
        SET processed_cosy = processed_cosy_temp;
    ELSE
        PROCESS DQF_COSY WITH "2d_cosy_abs_nus_no_sym.list" TO processed_cosy_temp SAVE AS "$(SAMPLE)_DQF_COSY$(fname_ext)_FT";
        SET processed_cosy = processed_cosy_temp;
    END IF;

    PRESENTATION dqf_cosy_pdf TEMPLATE "cosy_runtime_positive"
        WITH DATA processed_cosy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_DQF_COSY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH dqf_cosy AND dqf_cosy_pdf;

END METHOD "12. DQF COSY";

-------------------------------------------------------------------------------
-- METHOD "13. TOCSY" IS

-------------------------------------------------------------------------------

METHOD "14. NOESY" IS

    PURPOSE "Proton-Proton Dipolar correlation spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](noesy_sampling_density) / 100)) * noesy +
             
             
             240[s];

           VAR calculate_proton_90     : BOOLEAN         = FALSE;
           VAR force_tune              : BOOLEAN         = FALSE;
           VAR dual_tuned              : BOOLEAN         = FALSE;
           VAR autogain                : BOOLEAN         = TRUE;
           VAR receiver_gain           : Gain_Range      = 0;

    EXPOSE VAR proton_scans            : NUMBER          = 16,      HELP "Number of scans to perform";
           VAR proton_dummy_scans      : NUMBER          = 0;
           VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm], HELP "Sweep width";
           VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],    HELP "Pre-pulse delay for Proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    EXPOSE VAR perform_proton_clip     : BOOLEAN         = TRUE,    HELP "Optimize 1H sweep width and carrier offset";
    EXPOSE VAR noesy_scans             : NUMBER          = 4,       HELP "Number of scans to perform";
    EXPOSE VAR noesy_mix_time          : NUMBER          = 500[ms], HELP "mix time";
    EXPOSE VAR noesy_relaxation_delay  : NUMBER          = 1.5[s],  HELP "Pre-pulse delay for Cosy experiemnt";
           VAR noesy_x_points          : NUMBER          = 1024;
           VAR noesy_y_points          : SamplingPoints  = 256;
    EXPOSE VAR noesy_sampling_density  : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            scans            = proton_scans;
            recvr_gain       = receiver_gain;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            relaxation_delay = proton_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( noesy_y_points, noesy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_homo2d_phase.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_homo2d_phase_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT NOESY IS
        SAVE AS "$(SAMPLE)_NOESY$(fname_ext)";
        COLLECT "noesy_phase_pfgzz";
        SET * = params;
        SET scans            = noesy_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            mix_time         = noesy_mix_time;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            x_points         = noesy_x_points;
            y_points         = noesy_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = noesy_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE NOESY;

    VAR processed_noesy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS NOESY WITH "2d_homo2d_phase.list" TO processed_noesy_temp SAVE AS "$(SAMPLE)_NOESY_FT";
        SET processed_noesy = processed_noesy_temp;
    ELSE
        PROCESS NOESY WITH "2d_homo2d_phase_nus.list" TO processed_noesy_temp SAVE AS "$(SAMPLE)_NOESY$(fname_ext)_FT";
        SET processed_noesy = processed_noesy_temp;
    END IF;

    PRESENTATION noesy_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_noesy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_NOESY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH noesy AND noesy_pdf;

END METHOD "14. NOESY";

-------------------------------------------------------------------------------
METHOD "15. ROESY" IS

    PURPOSE "Proton-Proton Dipolar correlation spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](roesy_sampling_density) / 100)) * roesy +

             120[s];

           VAR calculate_proton_90     : BOOLEAN         = FALSE;
    		VAR force_tune              : BOOLEAN         = FALSE;
    		VAR dual_tuned              : BOOLEAN         = FALSE;
    		VAR autogain                : BOOLEAN         = TRUE;
    		VAR receiver_gain           : Gain_Range      = 0;

    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
           VAR proton_dummy_scans      : NUMBER          = 0;
           VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
           VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay for Proton experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    EXPOSE VAR perform_proton_clip     : BOOLEAN         = TRUE,     HELP "Optimize 1H sweep width and carrier offset";
    EXPOSE VAR roesy_scans             : NUMBER          = 4,        HELP "Number of scans to perform";
    EXPOSE VAR roesy_mix_time          : NUMBER          = 250[ms],  HELP "mix time";
           VAR roesy_spinlock_field    : Spinlock_field  = "4[kHz]";
    EXPOSE VAR roesy_relaxation_delay  : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for Cosy experiemnt";
           VAR roesy_x_points          : NUMBER          = 1024;
           VAR roesy_y_points          : SamplingPoints  = 256;
    EXPOSE VAR roesy_sampling_density  : SamplingDensity = 25;


    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            scans            = proton_scans;
            recvr_gain       = receiver_gain;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            relaxation_delay = proton_relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE Proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "x_offset set to $(proton_xoffset)";
        INFORM "x_sweep set to $(proton_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( roesy_y_points, roesy_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_homo2d_phase.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_homo2d_phase_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT ROESY IS
        SAVE AS "$(SAMPLE)_ROESY$(fname_ext)";
        COLLECT "roesy_phase";
        SET * = params;
        SET scans             = roesy_scans;
            comment           = comment;
            force_dual_mode   = dual_tuned;
            mix_time          = roesy_mix_time;
            spinlock_strength = roesy_spinlock_field;
            x_offset          = proton_xoffset;
            x_sweep           = proton_xsweep;
            x_points          = roesy_x_points;
            y_points          = roesy_y_points;
            recvr_gain        = proton("recvr_gain") + 4;
            relaxation_delay  = roesy_relaxation_delay;
            x_90_width        = proton_90;
            x_atn             = proton_atn;
    END EXPERIMENT;

    VISUALIZE ROESY;

    VAR processed_roesy : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS ROESY WITH "2d_homo2d_phase.list" TO processed_roesy_temp SAVE AS "$(SAMPLE)_ROESY_FT";
        SET processed_roesy = processed_roesy_temp;
    ELSE
        PROCESS ROESY WITH "2d_homo2d_phase_nus.list" TO processed_roesy_temp SAVE AS "$(SAMPLE)_ROESY$(fname_ext)_FT";
        SET processed_roesy = processed_roesy_temp;
    END IF;

    PRESENTATION roesy_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_roesy AND processed_proton AND processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_ROESY$(fname_ext).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH roesy AND roesy_pdf;

END METHOD "15. ROESY";

-------------------------------------------------------------------------------
-- METHOD "16. HMQC" IS

-------------------------------------------------------------------------------

METHOD "17. HSQC" IS

    PURPOSE "1H 13C Correlation Spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton  +
             (acquire_13c_data ? carbon : 0[s]) +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](hsqc_sampling_density) / 100)) * hsqc +
             
             240[s];

           VAR calculate_90s           : BOOLEAN         = FALSE;
           VAR force_tune              : BOOLEAN         = FALSE;
           VAR dual_tuned              : BOOLEAN         = FALSE;
           VAR proton_autogain         : BOOLEAN         = TRUE;
           VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
           VAR proton_dummy_scans      : NUMBER          = 0;
           VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
           VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay";

    EXPOSE VAR acquire_13c_data        : BOOLEAN         = FALSE,    HELP "Collect 13C data for high resolution projection";
           VAR carbon_autogain         : BOOLEAN         = TRUE;
           VAR carbon_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR carbon_scans            : NUMBER          = 256,      HELP "Number of scans to perform";
           VAR carbon_dummy_scans      : NUMBER          = 4;
           VAR carbon_tip_angle        : NUMBER          = 30[deg];
           VAR carbon_sn_ratio         : NUMBER          = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER          = 85[ppm],  DEPENDS ON acquire_13c_data EVALUATE (acquire_13c_data ? 100[ppm] : 85[ppm]);
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 170[ppm], DEPENDS ON acquire_13c_data EVALUATE (acquire_13c_data ? 250[ppm] : 170[ppm]);
           VAR carbon_data_points      : NUMBER          = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER          = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    EXPOSE VAR perform_proton_clip     : BOOLEAN         = TRUE,     HELP "Optimize 1H sweep width and carrier offset";
    EXPOSE VAR perform_carbon_clip     : BOOLEAN         = TRUE,     HELP "Optimize 13C sweep width and carrier offset";
    EXPOSE VAR hsqc_scans              : NUMBER          = 2,        HELP " Number of scans for HMQC experiment";
    EXPOSE VAR hsqc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HMQC experiment";
    EXPOSE VAR hsqc_x_points           : NUMBER          = 1024,     HELP "HMQC data points";
           VAR hsqc_y_points           : SamplingPoints  = 128;
    EXPOSE VAR hsqc_sampling_density   : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Carbon13";
    VAR irr_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;
    VAR carbon_xoffset   : NUMBER = carbon_x_offset;
    VAR carbon_xsweep    : NUMBER = carbon_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination if requested, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    VAR processed_carbon : DATA;
    VAR carbon_pdf       : DATA;

    IF acquire_13c_data THEN
        CONCEAL EXPERIMENT carbon IS
            SAVE AS "$(SAMPLE)_CARBON";
            COLLECT "carbon";
            SET auto_gain        = carbon_autogain;
                comment          = comment;
                force_dual_mode  = dual_tuned;
                process          = "carbon_autophase_p.list";
                relaxation_delay = carbon_relaxation_delay;
                scans            = carbon_scans;
                recvr_gain       = carbon_receiver_gain;
                sn_ratio         = carbon_sn_ratio;
                x_angle          = carbon_tip_angle;
                x_points         = carbon_data_points;
                x_prescans       = carbon_dummy_scans;
                x_offset         = carbon_x_offset;
                x_sweep          = carbon_x_sweep;
                x_90_width       = carbon_90;
                x_atn            = carbon_atn;
        END EXPERIMENT;

        VISUALIZE carbon;

        PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon_temp SAVE AS "$(SAMPLE)_CARBON_FT";
        SET processed_carbon = processed_carbon_temp;

        PRESENTATION carbon_pdf_temp TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_Carbon.pdf";
        SET carbon_pdf = carbon_pdf_temp;

        EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
        "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH carbon AND carbon_pdf;
    END IF;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF processed_carbon /= NULL AND perform_carbon_clip THEN
        INVOKE util.Handle_Clipping( processed_carbon, carbon_xoffset, carbon_xsweep );
        INFORM "Carbon y_offset set to $(carbon_xoffset)";
        INFORM "Carbon y_sweep set to $(carbon_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hsqc_y_points, hsqc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_inverse_pn.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_inverse_pn_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HSQC IS
        SAVE AS "$(SAMPLE)_HSQC";
        COLLECT "hsqc";
        SET * = params;
        SET scans            = hsqc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_xoffset;
            y_sweep          = carbon_xsweep;
            x_points         = hsqc_x_points;
            y_points         = hsqc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hsqc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HSQC;

    VAR processed_hsqc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HSQC WITH "2d_inverse_pn.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC_FT";
        SET processed_hsqc = processed_hsqc_temp;
    ELSE
        PROCESS HSQC WITH "2d_inverse_pn_nus.list" TO processed_hsqc_temp SAVE AS "$(SAMPLE)_HSQC$(fname_ext)_FT";
        SET processed_hsqc = processed_hsqc_temp;
    END IF;

    IF processed_carbon = NULL THEN
        SET processed_carbon = project( processed_hsqc);
    END IF;

    PRESENTATION hsqc_pdf TEMPLATE "cosy_runtime"
            WITH DATA processed_hsqc AND processed_proton AND processed_carbon
            TO JOB PRINTER AND FILE "$(SAMPLE)_HSQC.pdf";

        EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
        "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hsqc AND hsqc_pdf;

END METHOD "17. HSQC";

-------------------------------------------------------------------------------

METHOD "18. HMBC" IS

    PURPOSE "1H 13C Long Range Correlation Spectroscopy";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Proton  +
             (acquire_13c_data ? carbon : 0[s]) +
             ((linear_or_nus = "Linear") ? 1 : ([NUMERIC](hmbc_sampling_density) / 100)) * hmbc +
             
             240[s];


           VAR calculate_90s           : BOOLEAN         = FALSE;
           VAR force_tune              : BOOLEAN         = FALSE;
           VAR dual_tuned              : BOOLEAN         = FALSE;
           VAR proton_autogain         : BOOLEAN         = TRUE;
           VAR proton_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR proton_scans            : NUMBER          = 16,       HELP "Number of scans to perform";
           VAR proton_dummy_scans      : NUMBER          = 0;
           VAR proton_tip_angle        : NUMBER          = 45[deg];
    EXPOSE VAR proton_x_offset         : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR proton_x_sweep          : NUMBER          = 15[ppm],  HELP "Sweep width";
           VAR proton_data_points      : NUMBER          = 32768;
    EXPOSE VAR proton_relaxation_delay : NUMBER          = 4[s],     HELP "Pre-pulse delay";

    EXPOSE VAR acquire_13c_data        : BOOLEAN         = FALSE,    HELP "Collect 13C data for high resolution projection";
           VAR carbon_autogain         : BOOLEAN         = TRUE;
           VAR carbon_receiver_gain    : Gain_Range      = 0;
    EXPOSE VAR carbon_scans            : NUMBER          = 256,      HELP "Number of scans to perform";
           VAR carbon_dummy_scans      : NUMBER          = 4;
           VAR carbon_tip_angle        : NUMBER          = 30[deg];
           VAR carbon_sn_ratio         : NUMBER          = 0;
    EXPOSE VAR carbon_x_offset         : NUMBER          = 100[ppm], DEPENDS ON acquire_13c_data EVALUATE (acquire_13c_data ? 100[ppm] : 100[ppm]);
    EXPOSE VAR carbon_x_sweep          : NUMBER          = 200[ppm], DEPENDS ON acquire_13c_data EVALUATE (acquire_13c_data ? 250[ppm] : 200[ppm]);
           VAR carbon_data_points      : NUMBER          = 32768;
    EXPOSE VAR carbon_relaxation_delay : NUMBER          = 2[s],     HELP "Pre-pulse delay for carbon experiment";

    EXPOSE VAR linear_or_nus           : LinearNus       = "Nus";

    EXPOSE VAR perform_proton_clip     : BOOLEAN         = TRUE,     HELP "Optimize 1H sweep width and carrier offset";
    EXPOSE VAR perform_carbon_clip     : BOOLEAN         = TRUE,     HELP "Optimize 13C sweep width and carrier offset";
    EXPOSE VAR hmbc_scans              : NUMBER          = 4,        HELP " Number of scans for HMQC Experiment";
    EXPOSE VAR hmbc_relaxation_delay   : NUMBER          = 1.5[s],   HELP "Pre-pulse delay for HMQC experiment";
           VAR hmbc_x_points           : NUMBER          = 1024;
    EXPOSE VAR hmbc_y_points           : SamplingPoints  = 256,      HELP "t1 increments";
    EXPOSE VAR hmbc_sampling_density   : SamplingDensity = 25;

    VAR comment          : TEXT   = SAMPLE "comment";
    VAR nuslist_idx_base : NUMBER = 1;

    VAR obs_domain       : DOMS   = "Carbon13";
    VAR irr_domain       : DOMS   = "Proton";
    VAR oneh_coil        : TEXT   = "hf1";
    VAR before_tune_idler : TEXT    = NAMESPACE "system.probe_id_idler" ELSE "";

    VAR proton_xoffset   : NUMBER = proton_x_offset;
    VAR proton_xsweep    : NUMBER = proton_x_sweep;
    VAR carbon_xoffset   : NUMBER = carbon_x_offset;
    VAR carbon_xsweep    : NUMBER = carbon_x_sweep;

    IF proton_autogain = TRUE AND proton_receiver_gain = 0 THEN
        SET proton_receiver_gain = 46;
    END IF;

    IF carbon_autogain = TRUE AND carbon_receiver_gain = 0 THEN
        SET carbon_receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET carbon_x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET proton_x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_90s, proton_autogain, proton_receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_90s THEN
        SET proton_autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF SAMPLE "solvent" = "D2O" THEN
        SET calculate_90s = FALSE;
        INFORM "Solvent is D2O, skipping 13C pulse width determination if requested, continuing...";
    END IF;

    INVOKE util.Auto_13C_90_Degree( calculate_90s, carbon_autogain, carbon_receiver_gain, 90[deg], dual_tuned );

    IF calculate_90s THEN
        SET carbon_autogain = FALSE;
    END IF;

    VAR carbon_90  : NUMBER = SAMPLE "carbon_90";
    VAR carbon_atn : NUMBER = SAMPLE "carbon_atn";
    VAR carbon_rg  : NUMBER = SAMPLE "carbon_rg";

    IF proton_rg /= NULL THEN
        SET proton_receiver_gain = proton_rg;
    END IF;

    IF carbon_rg /= NULL THEN
        SET carbon_receiver_gain = carbon_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "proton";
        SET auto_gain        = proton_autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = proton_receiver_gain;
            relaxation_delay = proton_relaxation_delay;
            scans            = proton_scans;
            x_angle          = proton_tip_angle;
            x_offset         = proton_x_offset;
            x_sweep          = proton_x_sweep;
            x_points         = proton_data_points;
            x_prescans       = proton_dummy_scans;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE proton;

    PROCESS Proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";

    PRESENTATION proton_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_proton
        TO JOB PRINTER AND FILE "$(SAMPLE)_PROTON.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND proton_pdf;

    VAR processed_carbon : DATA;
    VAR carbon_pdf       : DATA;

    IF acquire_13c_data THEN
        CONCEAL EXPERIMENT carbon IS
            SAVE AS "$(SAMPLE)_CARBON";
            COLLECT "carbon";
            SET auto_gain        = carbon_autogain;
                comment          = comment;
                force_dual_mode  = dual_tuned;
                process          = "carbon_autophase_p.list";
                relaxation_delay = carbon_relaxation_delay;
                scans            = carbon_scans;
                recvr_gain       = carbon_receiver_gain;
                sn_ratio         = carbon_sn_ratio;
                x_angle          = carbon_tip_angle;
                x_points         = carbon_data_points;
                x_prescans       = carbon_dummy_scans;
                x_offset         = carbon_x_offset;
                x_sweep          = carbon_x_sweep;
                x_90_width       = carbon_90;
                x_atn            = carbon_atn;
        END EXPERIMENT;

        VISUALIZE carbon;

        PROCESS carbon WITH "carbon_autophase_p.list" TO processed_carbon_temp SAVE AS "$(SAMPLE)_CARBON_FT";
        SET processed_carbon = processed_carbon_temp;

        PRESENTATION carbon_pdf_temp TEMPLATE "params_right_runtime_carbon_full"
            WITH DATA processed_carbon
            TO JOB PRINTER AND FILE "$(SAMPLE)_Carbon.pdf";
        SET carbon_pdf = carbon_pdf_temp;

        EMAIL USER
            SUBJECT "Raw Data for sample $(SAMPLE)"
            MESSAGE
                "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
            ATTACH carbon AND carbon_pdf;
    END IF;

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    --  Call clip() here to set x_sweep and x_offset if highres exists ---
    IF perform_proton_clip THEN
        INVOKE util.Handle_Clipping( processed_proton, proton_xoffset, proton_xsweep );
        INFORM "Proton x_offset set to $(proton_xoffset)";
        INFORM "Proton x_sweep set to $(proton_xsweep)";
    END IF;

    IF processed_carbon /= NULL AND perform_carbon_clip THEN
        INVOKE util.Handle_Clipping( processed_carbon, carbon_xoffset, carbon_xsweep );
        INFORM "Carbon y_offset set to $(carbon_xoffset)";
        INFORM "Carbon y_sweep set to $(carbon_xsweep)";
    END IF;

    VAR y_nuslist : LIST = {};

    IF linear_or_nus = "Nus" THEN
        INVOKE util.y_nuslist( hmbc_y_points, hmbc_sampling_density, y_nuslist );
        INFORM "Setting non uniform sampling points to $(y_nuslist)";
    END IF;

    VAR params    : util.Assoc;
    VAR fname_ext : TEXT = "";

    IF linear_or_nus = "Linear" THEN
        SET params("process")          = "2d_hmbc_abs.list";
    ELSE
        SET params("y_nuslist")        = y_nuslist;
        SET params("nuslist_idx_base") = nuslist_idx_base;
        SET params("process")          = "2d_hmbc_abs_nus.list";
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HMBC IS
        SAVE AS "$(SAMPLE)_HMBC$(fname_ext)";
        COLLECT "hmbc_pfg";
        SET * = params;
        SET scans            = hmbc_scans;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = proton_xoffset;
            x_sweep          = proton_xsweep;
            y_offset         = carbon_xoffset;
            y_sweep          = carbon_xsweep;
            x_points         = hmbc_x_points;
            y_points         = hmbc_y_points;
            recvr_gain       = proton("recvr_gain") + 4;
            relaxation_delay = hmbc_relaxation_delay;
            x_pulse          = proton_90;
            x_atn            = proton_atn;
            y_pulse          = carbon_90;
            y_atn            = carbon_atn;
    END EXPERIMENT;

    VISUALIZE HMBC;

    VAR processed_hmbc : DATA;
    IF linear_or_nus = "Linear" THEN
        PROCESS HMBC WITH "2d_hmbc_abs.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC_FT";
        SET processed_hmbc = processed_hmbc_temp;
    ELSE
        PROCESS HMBC WITH "2d_hmbc_abs_nus.list" TO processed_hmbc_temp SAVE AS "$(SAMPLE)_HMBC$(fname_ext)_FT";
        SET processed_hmbc = processed_hmbc_temp;
    END IF;

    IF processed_carbon = NULL THEN
        SET processed_carbon = project( processed_hmbc);
    END IF;

    PRESENTATION hmbc_pdf TEMPLATE "cosy_runtime"
        WITH DATA processed_hmbc AND processed_proton AND processed_carbon
        TO JOB PRINTER AND FILE "$(SAMPLE)_HMBC.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH hmbc AND hmbc_pdf;

END METHOD "18. HMBC";

-------------------------------------------------------------------------------

METHOD "19. Selective NOESY 1D" IS

    PURPOSE "1D noe experiment";

    -- duration help "COLLECT statement experiment" + tune time + padding for gradient shimming"
    DURATION oned_noesy +
             (force_tune ? 60[s] : 0[s]) +
             120[s];

    EXPOSE VAR force_tune          : BOOLEAN    = TRUE,    HELP "Retune RF coil(s)";
    EXPOSE VAR dual_tuned          : BOOLEAN    = FALSE,   HELP "Dual tuning for HFX probes";
    EXPOSE VAR autogain            : BOOLEAN    = TRUE,    HELP "Optimize gain value automatically";
    EXPOSE VAR receiver_gain       : Gain_Range = 0,       DEPENDS ON autogain EVALUATE (autogain ? 0 : 46);
    EXPOSE VAR scans               : NUMBER     = 16,      HELP "Number of scans to perform, n*4";

    EXPOSE VAR excitation_offset   : NUMBER     = 5[ppm],  HELP "Offset to be excited";
    EXPOSE VAR selective_bandwidth : NUMBER     = 50[Hz],  HELP "Bandwidth of exciatation";
    EXPOSE VAR mix_time            : NUMBER     = 500[ms], HELP "Spin mixing time";

    EXPOSE VAR x_offset            : NUMBER     = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR x_sweep             : NUMBER     = 15[ppm], HELP "Sweep width";
    EXPOSE VAR data_points         : NUMBER     = 32768;
    EXPOSE VAR relaxation_delay    : NUMBER     = 4[s],    HELP "Pre-pulse delay";

    VAR comment     : TEXT   = SAMPLE "comment";
    VAR obs_domain  : DOMS   = "Proton";
    VAR oneh_coil   : TEXT   = "hf1";

    VAR obs_sel_180 : NUMBER = 20[ms];
    VAR obs_sel_atn : NUMBER = 60[dB];

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.gs();

    INVOKE util.Soft_pw_atn( selective_bandwidth, obs_sel_180, obs_sel_atn );
    INFORM "Gaussian pulse width set to $(obs_sel_180)";
    INFORM "Attenuator set to $(obs_sel_atn)";

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    CONCEAL EXPERIMENT oned_noesy IS
        SAVE AS "$(SAMPLE)_ONED_NOESY_OFFSET_$(excitation_offset)";
        COLLECT "noe_1d_dpfgse";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            mix_time         = mix_time;
            obs_sel_offset   = excitation_offset;
            obs_sel_180      = obs_sel_180;
            obs_sel_atn      = obs_sel_atn;
            process          = "proton_autophase.list";
            recvr_gain       = receiver_gain;
            scans            = scans;
            relaxation_delay = relaxation_delay;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = data_points;
    END EXPERIMENT;

    VISUALIZE oned_noesy;

    VAR tmp_noesy : DATA;
    SET tmp_noesy = phase( ppm( machinephase( fft( sexp( oned_noesy, 2[Hz], 0[s] ) ) ) ), 180, 0, 50[%] );
    PROCESS tmp_noesy WITH "null.list" to processed_noesy SAVE AS "$(SAMPLE)_ONED_NOESY_$(excitation_offset)_FT";

    PRESENTATION oned_noesy_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_noesy
        TO JOB PRINTER AND FILE "$(SAMPLE)_ONED_NOESY_$(excitation_offset).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH oned_noesy AND oned_noesy_pdf;

END METHOD "19. Selective NOESY 1D";

-------------------------------------------------------------------------------
-- METHOD "20. Selective TOCSY 1D" IS

-------------------------------------------------------------------------------

METHOD "21. Selective ROESY 1D" IS

    PURPOSE "1D noe experiment";

    -- duration help "COLLECT statement experiment" + tune time + padding for gradient shimming"
    DURATION oned_roesy +
             (force_tune ? 60[s] : 0[s]) +
             120[s];

    EXPOSE VAR force_tune          : BOOLEAN        = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE VAR dual_tuned          : BOOLEAN        = FALSE,    HELP "Dual tuning for HFX probes";
    EXPOSE VAR autogain            : BOOLEAN        = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE VAR receiver_gain       : Gain_Range     = 0,        DEPENDS ON autogain EVALUATE (autogain ? 0 : 46);
    EXPOSE VAR scans               : NUMBER         = 16,       HELP "Number of scans to perform, n*4";

    EXPOSE VAR excitation_offset   : NUMBER         = 5[ppm],   HELP "Offset to be excited";
    EXPOSE VAR selective_bandwidth : NUMBER         = 50[Hz],   HELP "Bandwidth of exciatation";
    EXPOSE VAR spinlock_strength   : Spinlock_field = "4[kHz]", HELP "Spin lock field";
    EXPOSE VAR mix_time            : NUMBER         = 250[ms],  HELP "Spin mixing time";


    EXPOSE VAR x_offset            : NUMBER         = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep             : NUMBER         = 15[ppm],  HELP "Sweep width";
    EXPOSE VAR data_points         : NUMBER         = 32768;
    EXPOSE VAR relaxation_delay    : NUMBER         = 4[s],     HELP "Pre-pulse delay";

    VAR comment     : TEXT   = SAMPLE "comment";
    VAR obs_domain  : DOMS   = "Proton";
    VAR oneh_coil   : TEXT   = "hf1";

    VAR obs_sel_180 : NUMBER = 20[ms];
    VAR obs_sel_atn : NUMBER = 60[dB];

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.gs();

    INVOKE util.Soft_pw_atn( selective_bandwidth, obs_sel_180, obs_sel_atn );
    INFORM "Gaussian pulse width set to $(obs_sel_180)";
    INFORM "Attenuator set to $(obs_sel_atn)";

    SET MACHINE PARAMETER "spin_state" = "SPIN OFF";

    CONCEAL EXPERIMENT oned_roesy IS
        SAVE AS "$(SAMPLE)_ONED_ROESY_OFFSET_$(excitation_offset)";
        COLLECT "roesy_1d_dpfgse";
        SET auto_gain         = autogain;
            comment           = comment;
            force_dual_mode   = dual_tuned;
            mix_time          = mix_time;
            obs_sel_offset    = excitation_offset;
            obs_sel_180       = obs_sel_180;
            obs_sel_atn       = obs_sel_atn;
            process           = "proton_autophase.list";
            recvr_gain        = receiver_gain;
            scans             = scans;
            spinlock_strength = spinlock_strength;
            relaxation_delay  = relaxation_delay;
            x_offset          = x_offset;
            x_sweep           = x_sweep;
            x_points          = data_points;
    END EXPERIMENT;

    VISUALIZE oned_roesy;

    VAR tmp_roesy : DATA;
    SET tmp_roesy = phase( ppm( machinephase( fft( sexp( oned_roesy, 2[Hz], 0[s] ) ) ) ), 180, 0, 50[%]);
    PROCESS tmp_roesy WITH "null.list" to processed_roesy SAVE AS "$(SAMPLE)_ONED_ROESY_$(excitation_offset)_FT";

    PRESENTATION oned_roesy_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_roesy
        TO JOB PRINTER AND FILE "$(SAMPLE)_ONED_ROESY_$(excitation_offset).pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH oned_roesy AND oned_roesy_pdf;

END METHOD "21. Selective ROESY 1D";

-------------------------------------------------------------------------------

METHOD "22. Presaturation" IS

    PURPOSE "Proton scout and Presaturation";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION proton +
             presaturation +
             (force_tune ? 60[s] : 0[s]) +
             (calculate_proton_90 ? 120[s] : 0[s]) +
             120[s];

    EXPOSE VAR calculate_proton_90 : BOOLEAN    = FALSE,   HELP "Calculate 90 degee pulse?";
    EXPOSE VAR force_tune          : BOOLEAN    = FALSE,   HELP "Retune RF coil(s)";
    EXPOSE VAR dual_tuned          : BOOLEAN    = FALSE,   HELP "Dual tuning for HFX probes";
    EXPOSE VAR autogain            : BOOLEAN    = TRUE,    HELP "Optimize gain value automatically";
    EXPOSE VAR receiver_gain       : Gain_Range = 0,       DEPENDS ON autogain EVALUATE (autogain ? 0 : 46);
    EXPOSE VAR proton_scans        : NUMBER     = 16,      HELP "Number of scans to perform";
    EXPOSE VAR x_offset            : NUMBER     = 5[ppm],  HELP "Center of spectrum";
    EXPOSE VAR x_sweep             : NUMBER     = 15[ppm], HELP "Sweep width";
    EXPOSE VAR relaxation_delay    : NUMBER     = 4[s],    HELP "Pre-pulse delay";
    EXPOSE VAR presat_scans        : NUMBER     = 16,      HELP "Number of scans to perform";
    EXPOSE VAR irr_attenuator      : NUMBER     = 40[dB],  HELP "Power level for presaturation";

    VAR comment    : TEXT = SAMPLE "comment";
    VAR obs_domain : DOMS = "Proton";
    VAR oneh_coil  : TEXT = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    IF autogain = TRUE AND receiver_gain = 0 THEN
        SET receiver_gain = 46;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.gs();

    INVOKE util.Auto_1H_90_Degree( calculate_proton_90, autogain, receiver_gain, 90[deg], dual_tuned, before_tune_idler );

    IF calculate_proton_90 THEN
        SET autogain = FALSE;
    END IF;

    VAR proton_90  : NUMBER = SAMPLE "proton_90";
    VAR proton_atn : NUMBER = SAMPLE "proton_atn";
    VAR proton_rg  : NUMBER = SAMPLE "proton_rg";

    IF proton_rg /= NULL THEN
        SET receiver_gain = proton_rg;
    END IF;

    CONCEAL EXPERIMENT proton IS
        SAVE AS "$(SAMPLE)_PROTON";
        COLLECT "single_pulse";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            recvr_gain       = receiver_gain;
            scans            = proton_scans;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            relaxation_delay = relaxation_delay;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VAR processed_proton : DATA;
    VAR high             : NUMBER;

    SET processed_proton = PROCESS proton WITH "scout.list";
        high             = CALL highest_peak( processed_proton );

    INFORM "Setting irr_offset to $(high)";

    CONCEAL EXPERIMENT presaturation IS
        SAVE AS "$(SAMPLE)_PRESATURATION";
        COLLECT "single_pulse";
        SET auto_gain        = TRUE;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "proton_autophase.list";
            x_offset         = proton("x_offset");
            x_sweep          = proton("x_sweep_clipped");
            relaxation_delay = relaxation_delay;
            x_prescans       = 4;
            scans            = presat_scans;
            irr_offset       = high;
            irr_mode         = "Presaturation";
            irr_attenuator   = irr_attenuator;
            x_90_width       = proton_90;
            x_atn            = proton_atn;
    END EXPERIMENT;

    VISUALIZE presaturation;

    PROCESS proton WITH "proton_autophase.list" TO processed_proton SAVE AS "$(SAMPLE)_PROTON_FT";
    PROCESS presaturation WITH "proton_autophase.list" TO processed_presaturation SAVE AS "$(SAMPLE)_PRESATURATION_FT";

    PRESENTATION presaturation_pdf TEMPLATE "presaturation_runtime_full"
        WITH DATA processed_proton and processed_presaturation
        TO JOB PRINTER AND FILE "$(SAMPLE)_Proton_Presaturation.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH proton AND presaturation AND presaturation_pdf;

END METHOD "22. Presaturation";

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METHOD "23. Fluorine" IS

    PURPOSE "Routine Fluorine single pulse experiment";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION Fluorine +
             (force_tune ? 60[s] : 0[s]) +
             120[s];

    EXPOSE VAR force_tune       : BOOLEAN = FALSE,     HELP "Retune RF coil(s)";
    EXPOSE VAR dual_tuned       : BOOLEAN = FALSE,     HELP "Dual tuning for HFX probes";
    EXPOSE VAR autogain         : BOOLEAN = TRUE,      HELP "Optimize gain value automatically";
    EXPOSE VAR scans            : NUMBER  = 16,        HELP "Number of scans to perform";
    EXPOSE VAR x_offset         : NUMBER  = -100[ppm], HELP "Center of spectrum";
    EXPOSE VAR x_sweep          : NUMBER  = 200[ppm],  HELP "Sweep width";
    EXPOSE VAR data_points      : NUMBER  = 32768,     HELP "Number of data points";
    EXPOSE VAR relaxation_delay : NUMBER  = 4[s],      HELP "Pre-pulse delay";

    VAR comment    : TEXT = SAMPLE "comment";
    VAR obs_domain : DOMS = "Fluorine19";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    --No need to determine coil for 19F as it is currently always on HF1
    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "HF1" DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.Set_1H_90_Params( before_tune_idler );

    INVOKE util.gs();

    CONCEAL EXPERIMENT Fluorine IS
        SAVE AS "$(SAMPLE)_Fluorine";
        COLLECT "single_pulse";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase.list";
            scans            = scans;
            relaxation_delay = relaxation_delay;
            x_domain         = "Fluorine19";
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = data_points;
    END EXPERIMENT;

    VISUALIZE Fluorine;

    PROCESS fluorine WITH "carbon_autophase.list" TO processed_fluorine SAVE AS "$(SAMPLE)_FLUORINE_FT";

    PRESENTATION fluorine_pdf TEMPLATE "params_right_runtime_proton_full"
        WITH DATA processed_fluorine
        TO JOB PRINTER AND FILE "$(SAMPLE)_FLUORINE.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH fluorine AND fluorine_pdf;

END METHOD "23. Fluorine";

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METHOD "24. Phosphorus" IS

    PURPOSE "Routine Phosphorus single pulse experiment";

    -- duration help "COLLECT statement experiment" + tune time + 90 degree calculation + padding for gradient shimming"
    DURATION phosphorus +
             (force_tune ? 60[s] : 0[s]) +
             120[s];

    EXPOSE VAR force_tune       : BOOLEAN = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE VAR dual_tuned       : BOOLEAN = FALSE,    HELP "Dual tuning for HFX probes";
    EXPOSE VAR autogain         : BOOLEAN = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE VAR scans            : NUMBER  = 64,       HELP "Number of scans to perform";
    EXPOSE VAR sn_ratio         : NUMBER  = 0,        HELP "Stop when s/n is achieved, 0 = skip test";
    EXPOSE VAR x_offset         : NUMBER  = 0[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep          : NUMBER  = 400[ppm], HELP "Sweep width";
    EXPOSE VAR data_points      : NUMBER  = 32768;
    EXPOSE VAR relaxation_delay : NUMBER  = 2[s],     HELP "Pre-pulse delay";

    VAR comment    : TEXT = SAMPLE "comment";
    VAR obs_domain : DOMS = "Phosphorus31";
    VAR irr_domain : DOMS = "Proton";
    VAR oneh_coil  : TEXT = "hf1";
    VAR before_tune_idler : TEXT = NAMESPACE "system.probe_id_idler" ELSE "";

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN obs_domain OFFSET x_offset
        COIL oneh_coil DOMAIN irr_domain OFFSET 5[ppm];

    INVOKE util.Set_1H_90_Params( before_tune_idler );

    INVOKE util.gs();

    CONCEAL EXPERIMENT phosphorus IS
        SAVE AS "$(SAMPLE)_PHOSPHORUS";
        COLLECT "single_pulse_dec";
        SET auto_gain        = autogain;
            comment          = comment;
            force_dual_mode  = dual_tuned;
            process          = "carbon_autophase_p.list";
            relaxation_delay = relaxation_delay;
            scans            = scans;
            sn_ratio         = sn_ratio;
            x_domain         = "Phosphorus31";
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = data_points;
    END EXPERIMENT;

    VISUALIZE phosphorus;

    PROCESS phosphorus WITH "carbon_autophase_p.list" TO processed_phosphorus SAVE AS "$(SAMPLE)_PHOSPHORUS_FT";

    PRESENTATION phosphorus_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA processed_phosphorus
        TO JOB PRINTER AND FILE "$(SAMPLE)_PHOSPHORUS.pdf";

    EMAIL USER
        SUBJECT "Raw Data for sample $(SAMPLE)"
        MESSAGE
            "Attached DATA and/or PDF. Finished collecting $(METHOD) with sample $(SAMPLE) on $(SITE)."
        ATTACH phosphorus AND phosphorus_pdf;

END METHOD "24. Phosphorus";

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