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ISIS Powder Diffraction Scripts - POLARIS Reference

Creating POLARIS 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 POLARIS 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 Polaris

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

polaris_example = Polaris(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
polaris_example = Polaris(config_file=config_file_path,
                          user_name="Mantid", ...)

Methods

The following methods can be executed on a POLARIS object:

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

create_vanadium

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 POLARIS the following parameters are required when executing create_vanadium:

The following may optionally be set.

Example

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

polaris_example.create_vanadium(calibration_mapping_file=cal_mapping_file,
                                mode="PDF", do_absorb_corrections=True,
                                first_cycle_run_no=100, 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 POLARIS the following parameters are required when executing focus:

The following parameters may also be optionally set:

Example

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

polaris_example.focus(calibration_mapping_file=cal_mapping_file,
                      mode="Rietveld", do_absorb_corrections=False,
                      file_ext=".s01", input_mode="Individual",
                      run_number="100-110")

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(...)

polaris_example.set_sample(sample=sample_obj)

create_total_scattering_pdf

Warning

Total scattering support is not yet fully implemented. Any results obtaining from using the below routine in its current state should not be considered accurate or complete.

The create_total_scattering_pdf method allows a user to create a Pair Distribution Function (PDF) from focused POLARIS data, with a view to performing further total scattering analysis.

This function takes as input a workspace group containing focussed data that has been normalized as a differential cross section. The input can be generated by running focus with van_normalisation_method=Absolute.

The function performs the following processing:

  • converts the x units of the workspace group containing the differential cross section to momentum transfer

  • calculates the Placzek self scattering algorithm using the workflow algorithm TotScatCalculateSelfScattering v1. This internally calculates a per detector Placzek correction using CalculatePlaczek v1 and then focusses the correction using GroupDetectors v2

  • subtracts the Placzek self scattering correction from the differential cross section

  • converts the differential cross-section into an \(S(Q) - 1\) distribution using the following equation. This is based on equations 5, 9 and 19 in [2]:

    \[S(Q) - 1 = (\frac{d\sigma_s}{d\Omega}(Q) - \langle\overline{b^2}\rangle) / \langle\overline{b}\rangle^2 = (\frac{d\sigma_s}{d\Omega}(Q) - \frac{\sigma_s}{4 \pi}) / \frac{\sigma_{coh}}{4 \pi}\]
    where \(\sigma_s\) is the total scattering cross section, \(\sigma_{coh}\) is the coherent scattering cross section, \(b\) is the scattering length.
    The angled brackets indicate averaging across chemical formula units while the overline indicates averaging across isotopes and spin states for an individual element

  • converts the \(S(Q) - 1\) distribution into a PDF using PDFFourierTransform v2

The input is specified using the run_number parameter. The input workspace group for this run number must either be loaded in Mantid with the naming format given by the focus method:

<run number>-Results-<TOF/D>

for example:

12345-Results-TOF

Or a focused file with the same name format must be in the output_directory specified when creating the POLARIS object.

The output PDF can be customized with the following parameters:

  • By calling with pdf_type the type of PDF output can be specified, with the option of G(r), g(r), RDF(r) (defaults to G(r)).

  • By calling with merge_banks=True a PDF will be generated based on the weighted sum of the detector banks performed using supplied Q limits q_lims=q_limits, q_limits can be in the form of an array or with shape (2, x) where x is the number of banks, or a string containing the directory of an appropriately formatted .lim file. To exclude any of the banks use -1 as the value for that bank in each list. By default or specifically called with merge_banks=False a PDF will be generated for each bank within the focused_workspace.

  • By calling with delta_q which will calculate the PDF after rebinning the Q workspace to have bin width delta_r.

  • By calling with delta_r which will calculate the PDF with bin width of delta_q.

  • By calling with lorch_filter will calculate the PDF with a Lorth Filter if set to True

  • By calling with freq_params a fourier filter will be performed on the focused signal removing any components from atomic distances outside of the parameters. The parameters must be given as list: [lower], or [lower, upper]. The upper bound serves to remove noise from the spectrum density, by default when a fourier filter is performed this is set to 1000 to minimise loss of detail while still being computationally efficient.

  • By calling with debug=True which will retain the intermediate self scattering correction workspace.

  • By calling with placzek_order the Placzek correction order can be specified, with the option of 1 or 2 (defaults to 1).

  • By calling with sample_temp the user can override the sample temperature provided in the logs. It defaults to using values from the logs if available.

Example

# Include all the banks
polaris_example.create_total_scattering_pdf(run_number='12345',
                                            merge_banks=True,
                                            q_lims=[[2.5, 3, 4, 6, 7], [3.5, 5, 7, 11, 40]],
                                            output_binning=[0,0.1,20],
                                            pdf_type='G(r)',
                                            freq_params=[1])

# Exclude the 2nd and 4th banks
polaris_example.create_total_scattering_pdf(run_number='12345',
                                            merge_banks=True,
                                            q_lims=[[2.5, -1, 4, -1, 7], [3.5, -1, 7, -1, 40]],
                                            output_binning=[0,0.1,20],
                                            pdf_type='G(r)',
                                            freq_params=[1])

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 POLARIS 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:
5    vanadium_run_numbers: "10"
6    empty_run_numbers: "20"
7  Rietveld:
8    vanadium_run_numbers: "30"
9    empty_run_numbers: "40"

Lines 5 and 6 in this example set the vanadium and empty run numbers for chopper off mode. Lines 8 and 9 set the vanadium and empty for chopper on mode.

Example

1-100:
  label: "1_1"
  offset_file_name: "offset_file.cal"
  PDF:
    vanadium_run_numbers: "10"
    empty_run_numbers: "20"
  Rietveld:
    vanadium_run_numbers: "30"
    empty_run_numbers: "40"

101-:
  label: "1_2"
  offset_file_name: "offset_file.cal"
  PDF:
    vanadium_run_numbers: "110"
    empty_run_numbers: "120"
  Rietveld:
    vanadium_run_numbers: "130"
    empty_run_numbers: "140"

Parameters

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

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)

  • Masking file (see: vanadium_peaks_masking_file)

  • 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:

polaris_example = Polaris(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
polaris_example = Polaris(calibration_mapping_file=r"C:\path\to\file\calibration_mapping.yaml", ...)

mode

optional

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 or Rietveld

Note: This parameter is not case sensitive

If this value is not set, mantid will attempt to deduce it from the frequency logs.

Example Input:

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

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
polaris_example = Polaris(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

Example Input:

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

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

do_van_normalisation

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:

polaris_example.focus(do_van_normalisation=True, ...)

van_normalisation_method

Indicates whether a relative or absolute normalisation should be performed. The possible values are “Relative” and “Absolute”.

This parameter is optional. The default value when mode =”Rietveld” is “Relative”. The default value when mode=”PDF” is “Absolute”.

If “Absolute” is selected then the measured intensity is multipled by the following additional factor to give a differential cross section (which is based on equation 8 in [1]):

\[\frac{\rho_v V_v \sigma_v}{4 \pi \rho_s V_s}\]

where \(\rho=\) number density, \(V=\) volume of material in the beam and the subscripts \(v\) and \(s\) indicate Vanadium and sample respectively.

Example Input:

polaris_example.focus(van_normalisation_method="Absolute", ...)

empty_can_subtraction_method

Sets the empty can subtraction type used in the focus method. This parameter is optional and can be set to either "Simple" (default) or "PaalmanPings". In "PaalmanPings" mode, the absorption correction is applied by PaalmanPingsMonteCarloAbsorption, followed by ApplyPaalmanPingsCorrection. Additionally, in this mode the paalman_pings_events_per_point parameter can be utilised.

Example Input:

polaris_example.focus(empty_can_subtraction_method="PaalmanPings", ...)

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:

polaris_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
polaris_example.create_vanadium(first_cycle_run_no=100, ...)

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:

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

multiple_scattering

optional

Indicates whether to account for the effects of multiple scattering when calculating absorption corrections.

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:

polaris_example.create_vanadium(multiple_scattering=True, ...)
# Or
polaris_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:

polaris_example = Polaris(output_directory=r"C:\path\to\output_dir", ...)

paalman_pings_events_per_point

Sets the number of EventsPerPoint to use in the PaalmanPingsMonteCarloAbsorption. The default value is 1000. This parameter is only used when empty_can_subtraction_method is set to "PaalmanPings".

Example Input:

polaris_example.focus(paalman_pings_events_per_point=10, ...)

per_detector_vanadium

Determines whether the Vanadium normalisation is performed at the detector level or the bank level. The default value is False (bank level). The parameter should be supplied to both the create_vanadium and focus methods (or supplied in the parameter list when creating the POLARIS object) if a reduction based on a per detector Vanadium normalisation is required.

from isis_powder import Polaris

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

polaris_example = Polaris(calibration_directory=calibration_dir,
                          output_directory=output_dir,
                          user_name="Mantid",
                          per_detector_vanadium=True)

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
polaris_example.focus(run_number="1, 3, 5-7", ...)
# Or just a single run
polaris_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.

Note: If this parameter is set to True sample_empty_scale must also be set. This is set to 1.0 by default.

Example Input:

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

suffix

Optional

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

Example Input:

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

user_name

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

Example Input:

polaris_example = Polaris(user_name="Mantid", ...)

Advanced Parameters

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.

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 POLARIS this is set to the following TOF windows:

focused_cropping_values = [
    (700,  30000),  # Bank 1
    (1200, 24900),  # Bank 2
    (1100, 19950),  # Bank 3
    (1100, 19950),  # Bank 4
    (1100, 19950),  # Bank 5
    ]

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 POLARIS this is set to the following:

grouping_file_name: "Master_copy_of_grouping_file_with_essential_masks.cal"

vanadium_peaks_masking_file

Determines the name of the masking file containing the masks to remove Bragg peaks on Polaris. This file must be located within the top level of the calibration_directory.

On POLARIS this is set to the following:

vanadium_peaks_masking_file: "VanaPeaks.dat"

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.

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
polaris_example.focus(sample_empty_scale=0.9, ...)

raw_data_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 POLARIS this is set to the following:

raw_data_cropping_values: (750, 20000)

spline_coefficient

Determines the spline coefficient to use when 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 POLARIS this is set to the following:

spline_coefficient: 100

spline_coeff_per_detector

Determines the spline coefficient to use when processing the vanadium in create_vanadium method. For more details see SplineBackground. This parameter is used if a detector level Vanadium normalisation has been requested and is typically lower than spline_coefficient

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

On POLARIS this is set to the following:

spline_coeff_per_detector: 10

vanadium_cropping_values

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_data_cropping_values.

On POLARIS this is set to the following:

vanadium_cropping_values = [(800, 19995),  # Bank 1
                            (800, 19995),  # Bank 2
                            (800, 19995),  # Bank 3
                            (800, 19995),  # Bank 4
                            (800, 19995),  # Bank 5
                           ]

Vanadium sample details

chemical_formula

The chemical formula for the Vanadium rod.

On POLARIS this is set to the following:

chemical_formula = "V"

cylinder_sample_height

The height of the Vanadium rod.

On POLARIS this is set to the following:

cylinder_sample_height = 4.0

cylinder_sample_radius

The radius of the Vanadium rod.

On POLARIS this is set to the following:

cylinder_sample_radius = 0.25

cylinder_position

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

On POLARIS this is set to the following:

cylinder_position = [0.0, 0.0, 0.0]

References

Category: Techniques