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# ISIS Powder Diffraction Scripts - GEM Reference¶

## Creating GEM Object¶

This method assumes you are familiar with the concept of objects in Python. If not more details can be read here: A quick introduction to objects

To create a GEM object the following parameters are required:

Optionally a configuration file may be specified if one exists using the following parameter:

See Using configuration files on YAML configuration files for more details

### Example¶

from isis_powder import Gem

calibration_dir = r"C:\path\to\calibration_dir"
output_dir = r"C:\path\to\output_dir"

gem_example = Gem(calibration_directory=calibration_dir,
output_directory=output_dir,
user_name="Mantid")

# Optionally we could provide a configuration file like so
# Notice how the file name ends with .yaml
config_file_path = r"C:\path\to\config_file.yaml
gem_example = Gem(config_file=config_file_path,
user_name="Mantid", ...)


## Methods¶

The following methods can be executed on a GEM object:

For information on creating a GEM object see: Creating GEM Object

The create_vanadium method allows a user to process a vanadium run. Whilst processing the vanadium run the scripts can apply any corrections the user enables and will spline the resulting workspace(s) for later focusing.

On GEM the following parameters are required when executing create_vanadium:

If do_absorb_corrections is set to True the following parameter is required in addition to the above:

#### Example¶

# Notice how the filename ends with .yaml
cal_mapping_file = r"C:\path\to\cal_mapping.yaml"

do_absorb_corrections=True,
first_cycle_run_no=100,
mode="PDF",
multiple_scattering=False)


### focus¶

The focus method processes the user specified run(s). It aligns, focuses and optionally applies corrections if the user has requested them.

On GEM the following parameters are required when executing focus:

If do_absorb_corrections is set to True the following parameter is required in addition to the above:

The following parameters may also be optionally set:

If sample_empty is set then the following parameter is also required:

#### Example¶

# Notice how the filename ends with .yaml
cal_mapping_file = r"C:\path\to\cal_mapping.yaml"

gem_example.focus(calibration_mapping_file=cal_mapping_file,
do_absorb_corrections=False,
file_ext=".s01", input_mode="Individual",
mode="Rietveld", run_number="100-105",


### set_sample¶

The set_sample method allows a user to specify a SampleDetails object which contains the sample properties used when do_absorb_corrections is True whilst focusing.

For more details on the SampleDetails object and how to set it see: ISIS Powder Diffraction Scripts - SampleDetails Reference

The following parameter is required when calling set_sample

• sample - This must be a SampleDetails object with the material set already.

#### Example¶

sample_obj = SampleDetails(...)
sample_obj.set_material(...)

gem_example.set_sample(sample=sample_obj)


### create_cal¶

The create_cal method creates the offset calibration file for GEM, or if one is passed in, adjusts an existing file. The following parameters are required:

The Following parameter may also be set

#### Example¶

# Notice how the filename ends with .yaml
cal_mapping_file = r"C:\path\to\cal_mapping.yaml"

gem_example.create_cal(run_number=87618,
calibration_mapping_file=cal_mapping_file)


## Calibration Mapping File¶

The calibration mapping file holds the mapping between run numbers, current label, offset filename and the empty and vanadium numbers.

For more details on the calibration mapping file see: Cycle mapping files

The layout on GEM should look as follows for each block substituting the below values for appropriate values:

11-100:
2  label: "1_1"
3  offset_file_name: "offset_file.cal"
4  PDF:
6    empty_run_numbers: "20"
7  Rietveld:
9    empty_run_numbers: "40"


Lines 5 and 6 in this example set the vanadium and empty run numbers for PDF mode. Lines 8 and 9 set the vanadium and empty for Rietveld mode.

### Example¶

1-100:
label: "1_1"
offset_file_name: "offset_file.cal"
PDF:
empty_run_numbers: "20"
Rietveld:
empty_run_numbers: "40"

101-:
label: "1_2"
offset_file_name: "offset_file.cal"
PDF:
empty_run_numbers: "120"
Rietveld:
empty_run_numbers: "140"


## Parameters¶

The following parameters for GEM are intended for regular use when using the ISIS Powder scripts.

Optional

This Parameter contains the path to an offsets .cal file to adjust using the automatic cal file generation.

### calibration_directory¶

This parameter should be the full path to the calibration folder. Within the folder the following should be present:

• Grouping .cal file (see: grouping_file_name)

• Folder(s) with the label name specified in mapping file (e.g. “1_1”) - Inside each folder should be the offset file with name specified in mapping file

The script will also save out vanadium splines into the relevant label folder which are subsequently loaded and used within the focus method.

Example Input:

gem_example = Gem(calibration_directory=r"C:\path\to\calibration_dir", ...)


### calibration_mapping_file¶

This parameter gives the full path to the YAML file containing the calibration mapping. For more details on this file see: Calibration Mapping File

Note: This should be the full path to the file including extension

Example Input:

# Notice the filename always ends in .yaml
gem_example = Gem(calibration_mapping_file=r"C:\path\to\file\calibration_mapping.yaml", ...)


### config_file¶

The full path to the YAML configuration file. This file is described in detail here: Using configuration files It is recommended to set this parameter at object creation instead of on a method as it will warn if any parameters are overridden in the scripting window.

Note: This should be the full path to the file including extension

Example Input:

# Notice the filename always ends in .yaml
gem_example = Gem(config_file=r"C:\path\to\file\configuration.yaml", ...)


### do_absorb_corrections¶

Indicates whether to perform vanadium absorption corrections in create_vanadium mode. In focus mode sample absorption corrections require the sample be set first with the set_sample method.

Accepted values are: True or False

Note: If this is set to ‘True’ multiple_scattering must be set

Example Input:

gem_example.create_vanadium(do_absorb_corrections=True, ...)

# Or (this assumes sample details have already been set)
gem_example.focus(do_absorb_corrections=True, ...)


### file_ext¶

Optional

Specifies a file extension to use when using the focus method.

This should be used to process partial runs. When processing full runs (i.e. completed runs) it should not be specified as Mantid will automatically determine the best extension to use.

Note: A leading dot (.) is not required but is preferred for readability

Example Input:

gem_example.focus(file_ext=".s01", ...)


### first_cycle_run_no¶

Indicates a run from the current cycle to use when calling create_vanadium. This does not have the be the first run of the cycle or the run number corresponding to the vanadium. However it must be in the correct cycle according to the Calibration Mapping File.

Example Input:

# In this example assume we mean a cycle with run numbers 100-200


### input_mode¶

Indicates how to interpret the parameter run_number whilst calling the focus method. If the input_mode is set to Summed it will process to sum all runs specified. If set to Individual it will process all runs individually (i.e. One at a time)

Accepted values are: Summed and Individual

Note: This parameter is not case sensitive

Example Input:

gem_example.focus(input_mode="Summed", ...)


### mode¶

The current chopper mode to use in the create_vanadium and focus method. This determines which vanadium and empty run numbers to use whilst processing.

Accepted values are: PDF and Rietveld

Note: This parameter is not case sensitive

Example Input:

gem_example.create_vanadium(mode="PDF", ...)
# Or
gem_example.focus(mode="Rietveld", ...)


### multiple_scattering¶

Indicates whether to account for the effects of multiple scattering when calculating absorption corrections. If do_absorb_corrections is set to True this parameter must be set.

Accepted values are: True or False

Note: Calculating multiple scattering effects will add around 10-30 minutes to the script runtime depending on the speed of the computer you are using

Example Input:

gem_example.create_vanadium(multiple_scattering=True, ...)
# Or
gem_example.focus(multiple_scattering=False, ...)


### output_directory¶

Specifies the path to the output directory to save resulting files into. The script will automatically create a folder with the label determined from the calibration_mapping_file and within that create another folder for the current user_name.

Within this folder processed data will be saved out in several formats.

Example Input:

gem_example = Gem(output_directory=r"C:\path\to\output_dir", ...)


### run_number¶

Specifies the run number(s) to process when calling the focus method.

This parameter accepts a single value or a range of values with the following syntax:

- : Indicates a range of runs inclusive (e.g. 1-10 would process 1, 2, 3….8, 9, 10)

, : Indicates a gap between runs (e.g. 1, 3, 5, 7 would process run numbers 1, 3, 5, 7)

These can be combined like so: 1-3, 5, 8-10 would process run numbers 1, 2, 3, 5, 8, 9, 10.

In addition the input_mode parameter determines what effect a range of inputs has on the data to be processed

Example Input:

# Process run number 1, 3, 5, 6, 7
gem_example.focus(run_number="1, 3, 5-7", ...)
# Or just a single run
gem_example.focus(run_number=100, ...)


### sample_empty¶

Optional

This parameter specifies a/several sample empty run(s) to subtract from the run in the focus method. If multiple runs are specified it will sum these runs before subtracting the result.

This input uses the same syntax as run_number. Please visit the above page for more details.

Example Input:

# Our sample empty is a single number
gem_example.focus(sample_empty=100, ...)
# Or a range of numbers
gem_example.focus(sample_empty="100-110", ...)


### sample_empty_scale¶

Required if sample_empty is set to True

Sets a factor to scale the sample empty run(s) to before subtracting. This value is multiplied after summing the sample empty runs and before subtracting the empty from the data set. For more details see: Scale.

Example Input:

# Scale sample empty to 90% of original
gem_example.focus(sample_empty_scale=0.9, ...)


### save_all¶

Optional

This parameter specifies whether or not all files should be saved on texture mode, if this is set to false then the .nxs and .gsas files will not be saved out. If unset then this defaults to True.

Example Input:

gem_example.focus(save_all=False, ...)


### texture_mode¶

If set to True, then this specifies that the reduction is to be carried out using Gem’s 160-bank texture mode, as opposed to the standard 6 banks. This means using altered cropping values for the vanadium and sample workspaces, and using Men Xie’s grouping file (which must be placed in the top level of your calibration_directory).

Example Input:

gem_example.focus(texture_mode=True, ...)


### unit_to_keep¶

Optional

Specifies a single unit to keep in Mantid after processing using the focus method. For example if dSpacing is set after processing only banks in d-spacing will be present.

Accepted values are: dSpacing and TOF

Note: All units will still be saved out in the output_directory regardless of this property

Note: This parameter is not case sensitive

Example Input:

gem_example.focus(unit_to_keep="dSpacing", ...)


### suffix¶

Optional

This parameter specifies a suffix to append the names of output files during a focus.

Example Input:

gem_example.focus(suffix="-corr", ...)


### user_name¶

Specifies the name of the current user when creating a new GEM object. This is only used when saving data to sort data into respective user folders. See output_directory for more details.

Example Input:

gem_example = Gem(user_name="Mantid", ...)


Indicates whether to divide the focused workspace within focus mode with a previously generated vanadium spline.

This requires a vanadium to have been previously created with the create_vanadium method

Accepted values are: True or False

Example Input:

gem_example.focus(vanadium_normalisation=True, ...)


Warning

These values are not intended to be changed and should reflect optimal defaults for the instrument. For more details please read: Instrument advanced properties

This section is mainly intended to act as reference of the current settings distributed with Mantid

All values changed in the advanced configuration file requires the user to restart Mantid for the new values to take effect. Please read Instrument advanced properties before proceeding to change values within the advanced configuration file.

### create_cal_rebin_1_params¶

The rebin parameters to use in the first rebin operation in create_cal. On GEM this is set to the following:

# Long mode OFF:
create_cal_rebin_1_params: "100,-0.0006,19950"


### create_cal_rebin_2_params¶

The rebin parameters to use in the second rebin operation in create_cal. On GEM this is set to the following:

create_cal_rebin_2_params: "1.05,0.002,1.3"


### cross_corr_reference_spectra¶

The Workspace Index of the spectra to correlate all other spectra against in the cross-correlation step of create_cal. On GEM this is set to the following:

cross_corr_reference_spectra: 5000


### cross_corr_ws_index_max¶

The workspace index of the last member of the range of spectra to cross-correlate against in create_cal. On GEM this is set to the following:

cross_corr_ws_index_max: 6450


### cross_corr_ws_index_min¶

The workspace index of the first member of the range of spectra to cross-correlate against in create_cal. On GEM this is set to the following:

cross_corr_ws_index_min: 11


### cross_cor_x_max¶

The ending point of the region to be cross correlated in create_cal. On GEM this is set to the following:

cross_corr_x_max: 1.3


### cross_cor_x_min¶

The starting point of the region to be cross correlated in create_cal. On GEM this is set to the following:

cross_corr_x_min: 1.0


### get_det_offsets_d_ref¶

Center of reference peak in d-space for GetDetectorOffsets in create_cal. On GEM this is set to the following:

get_det_offsets_d_ref: 1.912795


### get_det_offsets_step¶

Step size used to bin d-spacing data in GetDetectorOffsets when running create_cal. On GEM this is set to the following:

get_det_offsets_step: 0.002


### get_det_offsets_x_max¶

Maximum of CrossCorrelation data to search for peak, usually negative, in create_cal. On GEM this is set to the following:

get_det_offsets_x_max: 200


### get_det_offsets_x_min¶

Minimum of CrossCorrelation data to search for peak, usually negative, in create_cal. On GEM this is set to the following:

get_det_offsets_x_min: -200


### focused_cropping_values¶

Indicates a list of TOF values to crop the focused workspace which was created by focus on a bank by bank basis.

This parameter is a list of bank cropping values with one list entry per bank. The values must have a smaller TOF window than the vanadium_cropping_values

On GEM this is set to the following TOF windows:

# texture_mode = False (or not supplied)
focused_cropping_values = [(550, 19900),  # Bank 1
(550, 19900),  # Bank 2
(550, 19900),  # Bank 3
(550, 19900),  # Bank 4
(550, 19480),  # Bank 5
(550, 17980)   # Bank 6
]

# texture_mode = True
focused_cropping_values = [(448, 29344),  # Bank 1
(390, 19225),  # Bank 2
(390, 18673),  # Bank 3
...        # Too many to list here - see gem_advanced_config.py
(600, 16828),  # Bank 158
(600, 16822),  # Bank 159
(600, 16827)   # Bank 160
]


### grouping_file_name¶

Determines the name of the grouping cal file which is located within top level of the calibration_directory.

The grouping file determines the detector ID to bank mapping to use whilst focusing the spectra into banks.

On GEM this is set to the following:

# texture_mode = False (or not supplied)
grouping_file_name: "GEM_Instrument_grouping.cal"

# texture_mode = True
grouping_file_name: "offsets_xie_test_2.cal"


### gsas_calib_filename¶

The name of the GSAS calibration file used to generate MAUD input files when running a focus in texture_mode.

on GEM this is set to the following (this file is distributed with Mantid):

gsas_calib_filename: "GEM_PF1_PROFILE.IPF"


### nxs_filename¶

A template for the filename of the generated NeXus file.

### gss_filename¶

A template for the filename of the generated GSAS file.

### dat_files_directory¶

The subdirectory of the output directory where the .dat files are saved

### tof_xye_filename¶

A template for the filename of the generated TOF XYE file.

### dspacing_xye_filename¶

A template for the filename of the generated dSpacing XYE file.

### maud_grouping_scheme¶

When saving MAUD files (typically only done when running in texture_mode), there are too many banks to have calibration parameters for each bank. Instead, the normal 6-bank calibration file is used (see gsas_calib_filename), and each of the 160 texture banks is assigned the calibration parameters of one of the 6 banks in the file.

This parameter associates each of the 160 banks to one of the big banks. It is a list of bank IDs, where the value at element i is a number between 1 and 6, indicating which of the 6 banks to associate texture bank i with.

On GEM this is set to the following:

maud_grouping_scheme: [1] * 3 + [2] * 8 + [3] * 20 + [4] * 42 + [5] * 52 + [6] * 35


### raw_tof_cropping_values¶

Determines the TOF window to crop all spectra down to before any processing in the create_vanadium and focus methods.

This helps remove negative counts where at very low TOF the empty counts can exceed the captured neutron counts of the run to process.

On GEM this is set to the following:

raw_tof_cropping_values: (500, 20000)


### save_gda¶

If set to True, this saves the focused workspace to the MAUD-readable .gda format.

If texture_mode is set to True this is enabled, and disabled if it is set to False.

### save_maud_calib¶

If set to True, this uses the focus output and gsas_calib_filename to create a MAUD calibration file, using SaveGEMMAUDParamFile.

If texture_mode is set to True this is enabled, and disabled if it is set to False.

### save_maud¶

If set to True, this saves the focus output to the Maud three-column format (.gem file extension). If texture_mode is set to True this is enabled, and disabled if it is set to False.

### spline_coefficient¶

Determines the spline coefficient to use after processing the vanadium in create_vanadium method. For more details see: SplineBackground

Note that if this value is changed ‘create_vanadium’ will need to be called again.

On GEM this is set to the following:

spline_coefficient: 30


### subtract_empty_instrument¶

Provides the option to disable subtracting empty instrument runs from the run being focused. This is useful for focusing empties, as subtracting an empty from itself, or subtracting the previous cycle’s empty from this cycle’s, creates meaningless data. Set to False to disable empty subtraction.

On Gem this is set to the following:

subtract_empty_instrument: True


Determines the TOF windows to crop to on a bank by bank basis within the create_vanadium method. This is applied after focusing and before a spline is taken.

It is used to remove low counts at the start and end of the vanadium run to produce a spline which better matches the data.

This parameter is a list of bank cropping values with one list entry per bank. The values must have a larger TOF window than the focused_cropping_values and a smaller window than raw_tof_cropping_values.

On GEM this is set to the following:

# texture_mode = False (or not supplied)
vanadium_cropping_values = [(510, 19997),  # Bank 1
(510, 19997),  # Bank 2
(510, 19997),  # Bank 3
(510, 19997),  # Bank 4
(510, 19500),  # Bank 5
(510, 18000)   # Bank 6
]

# texture_mode = True
vanadium_cropping_values = [(75, 34933),   # Bank 1
(65, 22887),   # Bank 2
(65, 22230),   # Bank 3
...        # Too many banks to list here -see gem_advanced_config.py
(100, 20034),  # Bank 158
(100, 20026),  # Bank 159
(100, 20033)   # Bank 160
]


#### chemical_formula¶

The chemical formula for the Vanadium rod. This is a rod consisting of 94.86% Vanadium and 5.14% Niobium. Because this is not an elemental formula, number_density must also be set.

On GEM this is set to the following:

chemical_formula = "V0.9486 Nb0.0514"


#### number_density¶

The number density corresponding to the chemical_formula used. This is in units of atoms/Angstrom^3.

On GEM this is set to the following:

number_density = 0.071


#### cylinder_sample_height¶

The height of the Vanadium rod.

On GEM this is set to the following:

cylinder_sample_height = 4.0


On GEM this is set to the following:

cylinder_sample_radius = 0.4


#### cylinder_position¶

The position of the Vanadium rod in [x, y, z]

On GEM this is set to the following:

cylinder_position = [0.0, 0.0, 0.0]


Category: Techniques