-------------------------------------------------------------------------------
--                                                                           --
--                           Automation Script File                          --
--                Delta NMR Processing and Control Interface                 --
--                                                                           --
--         Copyright (c) 2009-2021 JEOL Ltd., All rights reserved            --
--                                                                           --
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
-- 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;

#sort methods FALSE

#define collection_mode = "Acq Time"

PURPOSE "A collection of common Methods for basic experimentation.";

INCLUDE "Utilities" TO DOMAIN util;

NUMBER Gain_Range IS INTEGER FROM -8 TO 102 STEP 2 WITH NO UNIT;

ENUM AUTO_SHIM_MODE IS ( "AUTSHIM OFF", "Z1 Z2", "Z1 Z3", "Z2 Z4", "Z1 Z4" );

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

ENUM dp_acq IS ("Acq Time", "Data Points");

ENUM MultiplicityEdit  IS ("up_down", "off", "CH_only");

NUMBER Peak_Range IS INTEGER FROM 1 TO 10 WITH NO UNIT;

ENUM WET_SOLVENTS IS NAMESPACE "solvent_reference.\"undeuterated names\"";

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

CONCEAL METHOD GET_WET_OFFSET( OUT found    : BOOLEAN;
                               OUT location : NUMBER;
                               IN  wet_solv : TEXT = "" ) IS
    PERCIVAL <<<
        function TRANSLATE_SOLVENT( solv : STRING ) return STRING is
            function GET_VALUE( path : STRING ) return WILDCARD is internal( "namespace_get_value" );

            var
                tmp_solv : STRING,
                solv_lst : SET := get_value( "solvent_reference.translation" );

            return solv when type solv_lst /= [SET];

            tmp_solv := solv_lst(solv);
            if tmp_solv = NULL and then size( solv ) = 16 then
                solv := upper( solv );
                for i : NUMERIC is 1 to size( solv_lst ) loop
                    if size( solv_lst(i,1) ) >= 16 and then
                       solv = upper( nth( solv_lst(i,1), 1, 16 ) ) then
                        tmp_solv := solv_lst(i,2);
                        exit;
                    end if;
                end loop;
            end if;
            if type tmp_solv /= [STRING] then
                return wet_solv;
            else
                return tmp_solv;
            end if;
        end TRANSLATE_SOLVENT;

        function GET_WET_OFS( solv : STRING ) return SET is
            function GET_VALUE( path : STRING ) return WILDCARD is internal( "namespace_get_value" );

            var
                wet_lst : SET := get_value( "solvent_reference.""1h"".""" & solv & """.peaks" ),
                ofs     : SET := {},
                loc     : WILDCARD;

            for i : NUMERIC is 1 to size( wet_lst ) loop
                ofs := ofs & {wet_lst(i, 1)};
            end loop;
            loc := sort( ofs )(1);
            return {loc /= NULL, loc};
        end GET_WET_OFS;
    >>>;

    VAR tr_solv : TEXT;
    VAR ret     : LIST;
    SET tr_solv  = call translate_solvent( wet_solv );
    SET ret      = call get_wet_ofs( tr_solv );
    SET found    = ret(1);
    SET location = ret(2);

END METHOD GET_WET_OFFSET;

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

MACRO proton_acq_conditions IS
    VAR x_points                  : NUMBER = 32768;
    EXPOSE PASSIVE VAR x_offset   : NUMBER = 5[ppm],             HELP "Center of spectrum";
    EXPOSE VAR x_sweep            : NUMBER = 15[ppm],            HELP "Sweep width";
    EXPOSE VAR collection_mode    : dp_acq = $(collection_mode), HELP "Select either data points or acquisition time";
    EXPOSE VAR points_or_acq_time : NUMBER = 2[s],               DEPENDS ON collection_mode EVALUATE ((collection_mode = "Data Points") ? 32768 : 2[s]), HELP "Adjust default data points or acquisition time";
    EXPOSE PASSIVE VAR x_angle    : NUMBER = 45[deg],            HELP "Tip angle";
    EXPOSE VAR relaxation_delay   : NUMBER = 5[s],               HELP "Pre-pulse delay for proton experiment";
END MACRO proton_acq_conditions;

MACRO carbon_acq_conditions IS
    VAR x_points                  : NUMBER = 32768;
    EXPOSE PASSIVE VAR x_offset   : NUMBER = 100[ppm],           HELP "Center of spectrum";
    EXPOSE VAR x_sweep            : NUMBER = 250[ppm],           HELP "Sweep width";
    EXPOSE VAR collection_mode    : dp_acq = $(collection_mode), HELP "Select either data points or acquisition time";
    EXPOSE VAR points_or_acq_time : NUMBER = 1[s],               DEPENDS ON collection_mode EVALUATE ((collection_mode = "Data Points") ? 32768 : 1[s]), HELP "Adjust default data points or acquisition time";
    EXPOSE PASSIVE VAR x_angle    : NUMBER = 30[deg],            HELP "Tip angle";
    EXPOSE VAR relaxation_delay   : NUMBER = 2[s],               HELP "Pre-pulse delay";
END MACRO carbon_acq_conditions;

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

METHOD Proton ( OUT highres_proton : DATA ) IS

    PURPOSE "Routine Proton single pulse experiment";

    DURATION Proton + ( force_tune ? 60[s] : 0[s] ) + 120[s];

    EXPOSE PASSIVE VAR comment  : TEXT       = "",    HELP "Enter a comment string";
    EXPOSE VAR force_tune       : BOOLEAN    = FALSE, HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain : BOOLEAN    = TRUE,  HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain    : Gain_Range = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";

    EXPAND MACRO proton_acq_conditions;

    EXPOSE VAR scans            : NUMBER     = 8;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

    IF collection_mode = "Acq Time" THEN
        INVOKE util.Determine_data_points( obs_domain, points_or_acq_time, x_sweep, x_points );
    ELSE
        SET x_points = points_or_acq_time;
    END IF;

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    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.Preamble();

    CONCEAL EXPERIMENT Proton IS
        SAVE AS "$(SAMPLE)_Proton";
        COLLECT "proton";
        SET process          = "proton_autophase.list";
            comment          = comment;
            auto_gain        = autogain;
            force_dual_mode  = dual_tuned;
            recvr_gain       = rgain;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = x_points;
            scans            = scans;
            x_angle          = x_angle;
            relaxation_delay = relaxation_delay;
            round_points     = FALSE;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = Proton("recvr_gain");

    PROCESS Proton TO highres_proton SAVE AS "$(SAMPLE)_Proton_ft";
    PROCESS Proton WITH "proton_autophase_pi.list" TO highres_proton2;

    PRESENTATION output_pdf TEMPLATE "params_right_runtime_proton_full"
            WITH DATA highres_proton2
            TO JOB PRINTER AND FILE "$(SAMPLE)_Proton_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "Proton", Proton, output_pdf );

END METHOD Proton;

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

METHOD Carbon ( OUT highres_carbon : DATA ) IS

    PURPOSE "Routine Carbon 1D spectrum";

    DURATION Carbon + ( force_tune ? 60[s] : 0[s] ) + 120[s];

    EXPOSE PASSIVE VAR comment  : TEXT    = "",    HELP "Enter a comment string";
    EXPOSE VAR force_tune       : BOOLEAN = FALSE, HELP "Retune RF coil(s)";

    EXPAND MACRO carbon_acq_conditions;

    EXPOSE VAR irr_noe          : BOOLEAN = TRUE, HELP "With or without NOE";
    EXPOSE PASSIVE VAR sn_ratio : NUMBER  = 0,    HELP "Stop acquisition when s/n ratio is achieved";
    EXPOSE VAR scans            : NUMBER  = 1024;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : DOMS    = "Carbon13";
    VAR irr_domain : DOMS    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

    IF collection_mode = "Acq Time" THEN
        INVOKE util.Determine_data_points( obs_domain, points_or_acq_time, x_sweep, x_points );
    ELSE
        SET x_points = points_or_acq_time;
    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.Preamble();

    CONCEAL EXPERIMENT Carbon IS
        SAVE AS "$(SAMPLE)_Carbon";
        COLLECT "carbon";
        SET process          = "carbon_autophase.list";
            comment          = comment;
            force_dual_mode  = dual_tuned;
            x_offset         = x_offset;
            x_sweep          = x_sweep;
            x_points         = x_points;
            scans            = scans;
            x_angle          = x_angle;
            relaxation_delay = relaxation_delay;
            irr_noe          = irr_noe;
            round_points     = FALSE;
            sn_ratio         = sn_ratio;
    END EXPERIMENT;

    PROCESS Carbon TO highres_carbon SAVE AS "$(SAMPLE)_Carbon_ft";
    PROCESS Carbon WITH "carbon_autophase_p.list" TO highres_carbon2;

    PRESENTATION output_pdf TEMPLATE "params_right_runtime_carbon_full"
        WITH DATA highres_carbon2
        TO JOB PRINTER AND FILE "$(SAMPLE)_Carbon_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "Carbon", Carbon, output_pdf );

END METHOD Carbon;

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

METHOD COSY ( CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Proton-Proton correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * COSY
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",       HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE,    HELP "Optimize sweep width and carrier offset";
    EXPOSE PASSIVE VAR x_offset     : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm],  HELP "Sweep width";
    EXPOSE VAR x_points             : NUMBER          = 1024,     HELP "Data pints for X axis";
    EXPOSE VAR y_points             : NUMBER          = 256,      HELP "Data pints for Y axis";
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR scans                : NUMBER          = 1;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
    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.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT COSY IS
        SAVE AS "$(SAMPLE)_COSY";
        COLLECT "cosy";
        SET *               = params;
        SET process         = "2d_cosy_abs.list";
            comment         = comment;
            auto_gain       = autogain;
            force_dual_mode = dual_tuned;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            x_points        = x_points;
            y_points        = y_points;
            recvr_gain      = rgain;
            scans           = scans;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = COSY("recvr_gain");

    PROCESS COSY TO outputdata SAVE AS "$(SAMPLE)_COSY$(fname_ext)_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata );
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_proton
            TO JOB PRINTER AND FILE "$(SAMPLE)_COSY_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "COSY", COSY, output_pdf );

END METHOD COSY;

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

METHOD TOCSY ( CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Proton-Proton mutli-bond correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * TOCSY
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",       HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE,    HELP "Optimize sweep width and carrier offset";
    EXPOSE PASSIVE VAR x_offset     : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm],  HELP "Sweep width";
    EXPOSE VAR x_points             : NUMBER          = 1024,     HELP "Data pints for X axis";
    EXPOSE VAR y_points             : NUMBER          = 256,      HELP "Data pints for Y axis";
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR mix_time             : NUMBER          = 50[ms],   HELP "mixing time of tocsy";
    EXPOSE VAR scans                : NUMBER          = 4;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
    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.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT TOCSY IS
        SAVE AS "$(SAMPLE)_TOCSY";
        COLLECT "tocsy";
        SET *               = params;
        SET process         = "2d_homo2d_phase.list";
            comment         = comment;
            auto_gain       = autogain;
            force_dual_mode = dual_tuned;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            x_points        = x_points;
            y_points        = y_points;
            recvr_gain      = rgain;
            scans           = scans;
            mix_time        = mix_time;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = TOCSY("recvr_gain");

    PROCESS TOCSY TO outputdata SAVE AS "$(SAMPLE)_TOCSY_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata );
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_proton
            TO JOB PRINTER AND FILE "$(SAMPLE)_TOCSY_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "TOCSY", TOCSY, output_pdf );

END METHOD TOCSY;

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

METHOD NOESY ( CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "NOE correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * NOESY
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",       HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE,    HELP "Optimize sweep width and carrier offset";
    EXPOSE PASSIVE VAR x_offset     : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm],  HELP "Sweep width";
    EXPOSE VAR x_points             : NUMBER          = 1024,     HELP "Data pints for X axis";
    EXPOSE VAR y_points             : NUMBER          = 256,      HELP "Data pints for Y axis";
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR mix_time             : NUMBER          = 1000[ms], HELP "Mixing time for NOESY (about T1)";
    EXPOSE VAR scans                : NUMBER          = 4;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
    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.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT NOESY IS
        SAVE AS "$(SAMPLE)_NOESY";
        COLLECT "noesy";
        SET *               = params;
        SET process         = "2d_homo2d_phase.list";
            comment         = comment;
            auto_gain       = autogain;
            force_dual_mode = dual_tuned;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            x_points        = x_points;
            y_points        = y_points;
            mix_time        = mix_time;
            scans           = scans;
            recvr_gain      = rgain;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = NOESY("recvr_gain");

    PROCESS NOESY TO outputdata SAVE AS "$(SAMPLE)_NOESY_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata );
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_proton
            TO JOB PRINTER and FILE "$(SAMPLE)_NOESY_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "NOESY", NOESY, output_pdf );

END METHOD NOESY;

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

METHOD ROESY ( CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Cross-relaxation correlation spectroscopy in the rotating frame";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * ROESY
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",       HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE,    HELP "Optimize sweep width and carrier offset";
    EXPOSE PASSIVE VAR x_offset     : NUMBER          = 5[ppm],   HELP "Center of spectrum";
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm],  HELP "Sweep width";
    EXPOSE VAR x_points             : NUMBER          = 1024,     HELP "Data pints for X axis";
    EXPOSE VAR y_points             : NUMBER          = 256,      HELP "Data pints for Y axis";
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR mix_time             : NUMBER          = 250[ms],  HELP "Mixing time for ROESY";
    EXPOSE VAR scans                : NUMBER          = 4;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
    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.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT ROESY IS
        SAVE AS "$(SAMPLE)_ROESY";
        COLLECT "roesy";
        SET *               = params;
        SET process         = "2d_homo2d_phase.list";
            comment         = comment;
            auto_gain       = autogain;
            force_dual_mode = dual_tuned;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            x_points        = x_points;
            y_points        = y_points;
            scans           = scans;
            mix_time        = mix_time;
            recvr_gain      = rgain;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = ROESY("recvr_gain");

    PROCESS ROESY TO outputdata SAVE AS "$(SAMPLE)_ROESY_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata );
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_proton
            TO JOB PRINTER and FILE "$(SAMPLE)_ROESY_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "ROESY", ROESY, output_pdf );

END METHOD ROESY;

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

NUMBER DEPT_Angles IS INTEGER FROM 45 TO 135 STEP 45 WITH UNIT [deg];

METHOD DEPT ( CONCEAL IN highres_carbon : DATA ) IS

    PURPOSE "DEPT experiment to distinguish CH, CH2, CH3 groups";

    DURATION DEPT + ( force_tune ? 60[s] : 0[s] ) + 120[s];

    EXPOSE PASSIVE VAR comment         : TEXT        = "",       HELP "Enter a comment string";
    EXPOSE VAR force_tune              : BOOLEAN     = FALSE,    HELP "Retune RF coil(s)";
    EXPAND MACRO carbon_acq_conditions;
    EXPOSE PASSIVE VAR selection_angle : DEPT_Angles = 135[deg], HELP "DEPT selection angle";
    EXPOSE VAR scans                   : NUMBER      = 512;

    VAR angle_value : TEXT    = [STRING](selection_angle`[]) & "deg";
    VAR dual_tuned  : BOOLEAN = FALSE;
    VAR obs_domain  : DOMS    = "Carbon13";
    VAR irr_domain  : DOMS    = "Proton";
    VAR oneh_coil   : TEXT    = "hf1";

    IF collection_mode = "Acq Time" THEN
        INVOKE util.Determine_data_points( obs_domain, points_or_acq_time, x_sweep, x_points );
    ELSE
        SET x_points = points_or_acq_time;
    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.Preamble();

    CONCEAL EXPERIMENT DEPT IS
        SAVE AS "$(SAMPLE)_DEPT$(angle_value)";
        COLLECT "dept_dec";
        SET process         = "dept_autophase_p.list";
            comment         = comment;
            force_dual_mode = dual_tuned;
            selection_angle = selection_angle;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            x_points        = x_points;
            scans           = scans;
    END EXPERIMENT;

    PROCESS DEPT TO outputdata SAVE AS "$(SAMPLE)_DEPT$(angle_value)_ft";

    PRESENTATION output_pdf TEMPLATE "params_right_runtime_carbon_full"
            WITH DATA outputdata
            TO JOB PRINTER AND FILE "$(SAMPLE)_DEPT$(angle_value)_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "DEPT$(angle_value)", DEPT, output_pdf );

END METHOD DEPT;

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

METHOD "Edited DEPT" IS

    PURPOSE "Edited DEPT";

    -- Begin Carbon section
    EXPOSE VAR force_tune       : BOOLEAN = FALSE,                HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR x_offset : NUMBER  = 100[ppm],             HELP "Center of spectrum";
    EXPOSE VAR x_sweep          : NUMBER  = 250[ppm],             HELP "Sweep width";
    EXPOSE PASSIVE VAR save_as  : TEXT    = "edited dept",        HELP "Basename of saved spectra";
    CONST carbon_save_as        : TEXT    = save_as & "_CARBON";
    EXPOSE VAR scans            : NUMBER  = 1024;

    VAR dual_tuned : BOOLEAN = FALSE;
    -- End Carbon section

    -- Begin DEPT45 section
    CONST dept_45_save_as  : TEXT = save_as & "_DEPT_45";
    -- End DEPT45 section

    -- Begin DEPT90 section
    CONST dept_90_save_as  : TEXT = save_as & "_DEPT_90";
    -- End DEPT90 section

    -- Begin DEPT135 section
    CONST dept_135_save_as : TEXT = save_as & "_DEPT_135";
    -- End DEPT135 section

    -- Common Block
    EXPOSE VAR save_edited_spectra : BOOLEAN = TRUE,  HELP "Save processed spectra";
    CONST pdf_filename             : TEXT    = save_as & "_EDITED_DEPT";
    -- End Common Block

    VAR dept_scans : NUMBER = scans / 2;
    VAR obs_domain : DOMS   = "Carbon13";
    VAR irr_domain : DOMS   = "Proton";
    VAR oneh_coil  : TEXT   = "hf1";

    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.Preamble();

    CONCEAL EXPERIMENT Carbon IS
        SAVE AS carbon_save_as;
        COLLECT "carbon";
        SET process         = "carbon_autophase_p.list";
            force_dual_mode = dual_tuned;
            scans           = scans;
            x_offset        = x_offset;
            x_sweep         = x_sweep;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_45 IS
        SAVE AS dept_45_save_as;
        COLLECT "dept_dec";
        SET scans           = dept_scans;
            CONSTRAIN scans MULTIPLE OF 8 INCREASE;
        SET selection_angle = 45[deg];
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            force_dual_mode = dual_tuned;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_90 IS
        SAVE AS dept_90_save_as;
        COLLECT "dept_dec";
        SET scans           = dept_scans;
            CONSTRAIN scans MULTIPLE OF 8 INCREASE;
        SET selection_angle = 90[deg];
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            force_dual_mode = dual_tuned;
    END EXPERIMENT;

    CONCEAL EXPERIMENT Dept_135 IS
        SAVE AS dept_135_save_as;
        COLLECT "dept_dec";
        SET scans           = dept_scans;
            CONSTRAIN scans MULTIPLE OF 8 INCREASE;
        SET selection_angle = 135[deg];
            x_offset        = x_offset;
            x_sweep         = x_sweep;
            force_dual_mode = dual_tuned;
    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 the can be linked to in PM that will allow the CHs 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 );

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

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

END METHOD "Edited DEPT";

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

METHOD HMQC ( CONCEAL IN highres_carbon : DATA;
              CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Inverse detected heteronuclear long-range correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * HMQC
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",    HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = TRUE, HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = FALSE, HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 50, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE, HELP "Optimize sweep width and carrier offset";
    EXPOSE VAR x_offset             : NUMBER          = 5[ppm];
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm];
    EXPOSE VAR x_points             : NUMBER          = 1024;
    EXPOSE VAR y_offset             : NUMBER          = 85[ppm];
    EXPOSE VAR y_sweep              : NUMBER          = 170[ppm];
    EXPOSE VAR y_points             : NUMBER          = 256;
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR j_constant           : NUMBER          = 140[Hz];
    EXPOSE VAR scans                : NUMBER          = 4;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : DOMS    = "Proton";
    VAR irr_domain : DOMS    = "Carbon13";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
        IF highres_carbon /= NULL THEN
            INVOKE util.Handle_Clipping(highres_carbon, y_offset, y_sweep);
            INFORM "y_offset set to $(y_offset)";
            INFORM "y_sweep set to $(y_sweep)";
        END IF;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN irr_domain OFFSET y_offset
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HMQC IS
        SAVE AS "$(SAMPLE)_HMQC";
        COLLECT "hmqc";
        SET *               = params;        
        SET process         = "2d_inverse_abs.list";
            comment         = comment;
            force_dual_mode = dual_tuned;
            auto_gain       = autogain;
            recvr_gain      = rgain;
            x_sweep         = x_sweep;
            x_offset        = x_offset;
            x_points        = x_points;
            y_sweep         = y_sweep;
            y_offset        = y_offset;
            y_points        = y_points;
            scans           = scans;
            j_constant      = j_constant;
    END EXPERIMENT;

    PROCESS HMQC TO outputdata SAVE AS "$(SAMPLE)_HMQC_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata,2);
    END IF;

    IF highres_carbon = NULL THEN
        SET highres_carbon = project( outputdata);
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_carbon
            TO JOB PRINTER and FILE "$(SAMPLE)_HMQC_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "HMQC", HMQC, output_pdf );

END METHOD HMQC;

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

METHOD "HSQC" ( CONCEAL IN highres_carbon : DATA;
                CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Inverse detected heteronuclear correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * HSQC
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment        : TEXT             = "",    HELP "Enter a comment string";
    EXPOSE VAR force_tune             : BOOLEAN          = TRUE, HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain       : BOOLEAN          = FALSE, HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain          : Gain_Range       = 50, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip   : BOOLEAN          = FALSE, HELP "Optimize sweep width and carrier offset";
    EXPOSE VAR x_offset               : NUMBER           = 5[ppm];
    EXPOSE VAR x_sweep                : NUMBER           = 15[ppm];
    EXPOSE VAR x_points               : NUMBER           = 1024;
    EXPOSE VAR y_offset               : NUMBER           = 85[ppm];
    EXPOSE VAR y_sweep                : NUMBER           = 170[ppm];
    EXPOSE VAR y_points               : NUMBER           =  128;
    EXPOSE VAR linear_or_nus          : util.LinearNus   = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density       : util.NusDensity  = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR multiplicity_edit_mode : MultiplicityEdit = "up_down";
    EXPOSE VAR scans                  : NUMBER           = 2;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : DOMS    = "Proton";
    VAR irr_domain : DOMS    = "Carbon13";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
        IF highres_carbon /= NULL THEN
            INVOKE util.Handle_Clipping(highres_carbon, y_offset, y_sweep);
            INFORM "y_offset set to $(y_offset)";
            INFORM "y_sweep set to $(y_sweep)";
        END IF;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN irr_domain OFFSET y_offset
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.Preamble();

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HSQC IS
        SAVE AS "$(SAMPLE)_HSQC";
        COLLECT "hsqc";
        SET *                      = params;
        SET process                = "2d_inverse_phase.list";
            comment                = comment;
            force_dual_mode        = dual_tuned;
            auto_gain              = autogain;
            recvr_gain             = rgain;
            x_offset               = x_offset;
            x_sweep                = x_sweep;
            x_points               = x_points;
            y_offset               = y_offset;
            y_sweep                = y_sweep;
            y_points               = y_points;
            scans                  = scans;
            multiplicity_edit_mode = multiplicity_edit_mode;
    END EXPERIMENT;

    PROCESS HSQC TO outputdata SAVE AS "$(SAMPLE)_HSQC_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata,2);
    END IF;

    IF highres_carbon = NULL THEN
        SET highres_carbon = project( outputdata);
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_carbon
            TO JOB PRINTER and FILE "$(SAMPLE)_HSQC_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "HSQC", HSQC, output_pdf );

END METHOD "HSQC";

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

METHOD HMBC ( CONCEAL IN highres_carbon : DATA;
              CONCEAL IN highres_proton : DATA ) IS

    PURPOSE "Inverse detected heteronuclear long-range correlation spectroscopy";

    DURATION (( linear_or_nus = "Linear" ) ? 1 : sampling_density / 100) * HMBC
             + ( force_tune ? 60[s] : 0[s] )
             + 120[s];

    EXPOSE PASSIVE VAR comment      : TEXT            = "",      HELP "Enter a comment string";
    EXPOSE VAR force_tune           : BOOLEAN         = FALSE,   HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain     : BOOLEAN         = FALSE,   HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain        : Gain_Range      = 50, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE PASSIVE VAR perform_clip : BOOLEAN         = FALSE,   HELP "Optimize sweep width and carrier offset";
    EXPOSE VAR x_offset             : NUMBER          = 5[ppm];
    EXPOSE VAR x_sweep              : NUMBER          = 15[ppm];
    EXPOSE VAR x_points             : NUMBER          = 1024;
    EXPOSE VAR y_offset             : NUMBER          = 100[ppm];
    EXPOSE VAR y_sweep              : NUMBER          = 250[ppm];
    EXPOSE VAR y_points             : NUMBER          = 256;
    EXPOSE VAR linear_or_nus        : util.LinearNus  = "Linear", HELP "Select monotonic increments (Linear) or Non Uniform Sampling";
    EXPOSE VAR sampling_density     : util.NusDensity = 25, DEPENDS ON linear_or_nus ENABLE WHEN (linear_or_nus = "Nus"), HELP "Non Uniform Sampling sampling density";
    EXPOSE VAR longrange_j          : NUMBER          = 8[Hz];
    EXPOSE VAR scans                : NUMBER          = 4;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : DOMS    = "Proton";
    VAR irr_domain : DOMS    = "Carbon13";
    VAR oneh_coil  : TEXT    = "hf1";

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

    --  Call clip() here to set x_sweep and x_offset if highres exists --
    IF perform_clip THEN
        IF highres_proton /= NULL THEN
            INVOKE util.Handle_Clipping(highres_proton, x_offset, x_sweep);
            INFORM "x_offset set to $(x_offset)";
            INFORM "x_sweep set to $(x_sweep)";
        END IF;
        IF highres_carbon /= NULL THEN
            INVOKE util.Handle_Clipping(highres_carbon, y_offset, y_sweep);
            INFORM "y_offset set to $(y_offset)";
            INFORM "y_sweep set to $(y_sweep)";
        END IF;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    TUNE PROBE FORCE force_tune DUAL dual_tuned
        COIL "LF1"     DOMAIN irr_domain OFFSET y_offset
        COIL oneh_coil DOMAIN obs_domain OFFSET x_offset;

    INVOKE util.Preamble();

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

    INVOKE util.NUS_Params( params, linear_or_nus, sampling_density );
    IF linear_or_nus = "Nus" THEN
        SET fname_ext = "_NUS";
    END IF;

    CONCEAL EXPERIMENT HMBC IS
        SAVE AS "$(SAMPLE)_HMBC";
        COLLECT "hmbc";
        SET *               = params;
        SET process         = "2d_hmbc_abs.list";
            comment         = comment;
            auto_gain       = autogain;
            force_dual_mode = dual_tuned;
            recvr_gain      = rgain;
            x_sweep         = x_sweep;
            x_offset        = x_offset;
            x_points        = x_points;
            y_sweep         = y_sweep;
            y_offset        = y_offset;
            y_points        = y_points;
            scans           = scans;
            longrange_j     = longrange_j;
    END EXPERIMENT;

    PROCESS HMBC TO outputdata SAVE AS "$(SAMPLE)_HMBC_ft";

    IF highres_proton = NULL THEN
        SET highres_proton = project( outputdata,2);
    END IF;

    IF highres_carbon = NULL THEN
        SET highres_carbon = project( outputdata);
    END IF;

    PRESENTATION output_pdf TEMPLATE "cosy_runtime"
            WITH DATA outputdata AND highres_proton AND highres_carbon
            TO JOB PRINTER and FILE "$(SAMPLE)_HMBC_Presentation_$(JOB_ID).pdf";

    INVOKE util.Postamble( "HMBC", HMBC, output_pdf );

END METHOD HMBC;

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

METHOD Proton_VT ( OUT highres_proton : DATA ) IS

    PURPOSE "Routine Proton single pulse experiment with VT";

    EXPOSE PASSIVE VAR comment        : TEXT             = "",         HELP "Enter a comment string";
    EXPOSE VAR force_tune             : BOOLEAN          = TRUE,       HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain       : BOOLEAN          = TRUE,       HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain          : NUMBER           = NULL,       HELP "Observation receiver gain"; 
    EXPOSE PASSIVE VAR VT_target_list : LIST             = {30[dC], 40[dC], 50[dC], 60[dC]}, HELP "Target temperature";
    EXPOSE VAR VT_delay               : NUMBER           = 600[s],     HELP "How long to wait after temperature settles";
    EXPOSE PASSIVE VAR temp           : util.Temp_States = "TEMP ON",  HELP "Temp state for sample";
    EXPOSE PASSIVE VAR spin           : util.Spin_States = "SPIN ON",  HELP "Spin state for sample";
                   VAR lock           : util.Lock_States = "AUTOLOCK";
    EXPAND MACRO proton_acq_conditions;
    EXPOSE PASSIVE VAR grad_shim      : BOOLEAN          = TRUE,       HELP "Force gradient shimming to be done";
    EXPOSE PASSIVE VAR auto_shim      : AUTO_SHIM_MODE   = "Z1 Z2",    HELP "Auto Shim mode";
    EXPOSE PASSIVE VAR save_to_sample : BOOLEAN          = TRUE,       HELP "Record the specified parameters to the Sample";
    EXPOSE VAR scans                  : NUMBER           = 8;

    VAR prefix     : TEXT   = NAMESPACE "lock.solvent_prefix";
    VAR temp_limit : NUMBER = NAMESPACE "$(prefix).\"$(SAMPLE.solvent)\".temp_boiling";
    VAR VT_target  : NUMBER;
    VAR loop_count : NUMBER = size( VT_target_list );
    VAR i          : NUMBER = 0;
    VAR tmp_gain   : NUMBER;

    VAR dual_tuned : BOOLEAN = FALSE;
    VAR obs_domain : TEXT    = "Proton";
    VAR oneh_coil  : TEXT    = "hf1";

    IF collection_mode = "Acq Time" THEN
        INVOKE util.Determine_data_points( obs_domain, points_or_acq_time, x_sweep, x_points );
    ELSE
        SET x_points = points_or_acq_time;
    END IF;

    INVOKE util.Determine_coil( oneh_coil );

    REPEAT loop_count TIMES DO
        SET i = i + 1;
        SET VT_target = VT_target_list(i);

        IF VT_target > temp_limit THEN
            INFORM FATAL "VT_target $(VT_target) is above boiling temperature $(temp_limit), skipping ...";
        ELSE
            INFORM "VT_target = $(VT_target)";
            INVOKE util.Set_State( VT_target, VT_delay, temp, spin, lock, save_to_sample );

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

            IF grad_shim THEN
                INVOKE util."Gradient Shim"();
                INVOKE util.Gradient_Shim( TRUE, TRUE, FALSE, TRUE, "1D" );
            END IF;

            IF auto_shim /= "AUTSHIM OFF" THEN
                SET NAMESPACE "parameter.autoshim_mode" = auto_shim;
                PROMOTE       "parameter.autoshim_mode" TO USER;
                PROMOTE SHIMS TO SAMPLE;
            END IF;

            IF autogain AND i > 1 THEN
                SET tmp_gain = SAMPLE "receiver_gain";
                IF tmp_gain /= NULL THEN
                    SET autogain = FALSE;
                    SET rgain    = tmp_gain;
                END IF;
            END IF;

            CONCEAL EXPERIMENT Proton  IS
                SAVE AS "$(SAMPLE)_Proton_$(VT_target)";
                COLLECT "proton";
                SET process         = "proton_autophase.list";
                    comment         = comment;
                    auto_gain       = autogain;
                    force_dual_mode = dual_tuned;
                    recvr_gain      = rgain;
                    x_offset        = x_offset;
                    x_sweep         = x_sweep;
                    x_points        = x_points;
                    scans           = scans;
            END EXPERIMENT;

            SET SAMPLE "receiver_gain" = Proton("recvr_gain");

            INVOKE util.Postamble( "Proton_$(VT_target)", Proton, NULL );
        END IF;
    END REPEAT;

END METHOD Proton_VT;

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METHOD "Proton No-D" ( CONCEAL INOUT peaklist : LIST = {} ) IS

    VAR processed_scout : DATA;
    VAR scout_params    : util.Assoc;

    EXPOSE VAR comment             : TEXT         = "",       HELP "Enter a comment string";
    EXPOSE VAR wet_solvent         : WET_SOLVENTS = "CHLOROFORM";
    EXPOSE VAR peaks               : Peak_Range   = 1,        HELP "Maximum number of peaks is 10";
    EXPOSE VAR force_tune          : BOOLEAN      = FALSE,    HELP "Retune RF coil(s)";
    EXPOSE PASSIVE VAR autogain    : BOOLEAN      = TRUE,     HELP "Optimize gain value automatically";
    EXPOSE PASSIVE VAR rgain       : Gain_Range   = 0, DEPENDS ON autogain EVALUATE (autogain ? 0 : 50) ENABLE WHEN (autogain = FALSE), HELP "Field will enable when proton_autogain is False";
    EXPOSE VAR scans               : NUMBER       = 8,        HELP "Number of scans to perform";
    EXPOSE VAR wet_pulse_bandwidth : NUMBER       = 0.2[ppm], HELP "Bandwidth of wet pulse";

    INVOKE util.Preamble();

    SET scout_params               = {};
        scout_params("auto_gain")  = TRUE;
        scout_params("process")    = "scout.list";
        scout_params("scans")      = 1;
        scout_params("sexp_width") = 20[Hz];

    IF autogain = TRUE AND rgain = 0 THEN
        SET rgain = 50;
    END IF;

    IF peaklist = {} THEN
        CONCEAL SCOUT EXPERIMENT scout_data IS
            SAVE AS "$(SAMPLE)_scout_scan";
            COLLECT "single_pulse";
            SET * = scout_params;
        END EXPERIMENT;

        INVOKE util.Insert_File_Parameters( scout_data, scout_params );

        SET processed_scout = PROCESS scout_data;
            peaklist        = CALL highest_peaks( processed_scout, peaks );
    END IF;

    INFORM "Peak positions are $(peaklist)";

    CONCEAL EXPERIMENT WET1D IS
        SAVE AS "$(SAMPLE)_1D_WET";
        COLLECT "single_pulse_wet";
        SET
            process       = "nod_wet1d.list";
            comment       = comment;
            force_tune    = force_tune;
            auto_gain     = autogain;
            recvr_gain    = rgain;
            scans         = scans;
            wet_number    = peaks;
            wet_solvent   = wet_solvent;
            soft_bw_input = wet_pulse_bandwidth;
            wet_slp       = peaklist;
    END EXPERIMENT;

    SET SAMPLE "receiver_gain" = WET1D("recvr_gain");

    VAR found : BOOLEAN;
    VAR loc   : NUMBER;
    INVOKE GET_WET_OFFSET( found, loc, wet_solvent );
    IF found THEN
        VAR wet_ofs : util.Assoc;
        SET wet_ofs                   = {};
            wet_ofs("wet_ref_offset") = loc;
        INVOKE util.Insert_File_Parameters( WET1D, wet_ofs );
    END IF;

    PROCESS WET1D WITH "nod_wet1d.list" TO outputdata SAVE AS "$(SAMPLE)_1D_WET_FT";

    INVOKE util.Postamble( "1D WET", WET1D );

END METHOD "Proton No-D";

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