StoG¶
This module defines the StoG class that tries to replicate the previous stog program behavior in an organized fashion with the ability to re-construct the workflow.
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class
pystog.stog.
StoG
(**kwargs)[source]¶ The StoG class is used to put together the Converter, Transformer, and FourierFilter class functionalities to reproduce the original stog Fortran program behavior. This class is meant to put together the functionality of the classes into higher-level calls to construct workflows for merging and processing multiple recprical space functions into a final output real space function.
This pythonized-version of the original Fortran stog uses numpy for data storage, organization, and manipulation “under the hood”.
Examples: >>> import json >>> from pystog import StoG >>> with open("../data/examples/argon_pystog.json", 'r') as f: >>> kwargs = json.load(f) >>> stog = StoG(**kwargs) >>> stog.read_all_data() >>> stog.merge_data() >>> stog.write_out_merged_data()
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GKofR_title
¶ The title of the with all corrections applied.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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add_dataset
(info, yscale=1.0, yoffset=0.0, xoffset=0.0, ydecimals=16, **kwargs)[source]¶ Takes the info with the dataset and manipulations, such as scales, offsets, cropping, etc., and creates an invidual numpy array for the pattern.
Parameters: - info (dict) – Dict with information for dataset (filename, manipulations, etc.)
- yscale (float) – Scale factor for the Y data (i.e. , , etc.)
- yoffset (float) – Offset factor for the Y data (i.e. , , etc.)
- xoffset – Offset factor for the X data (i.e. )
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append_file
(new_file)[source]¶ Appends a file to the file list
Parameters: new_file (str) – New file name to append Returns: File list with appended new_file Return type: list
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apply_lorch
(q, sq, r)[source]¶ Performs the Fourier transform using the Lorch dampening correction on the merged from the sq_master dictionary to generate the desired real space function with this correction. The results from both reciprocal space and real space are:
- Saved back to the respective “master” dictionaries
- Saved to files via the stem_name
- Returned from function
Parameters: - q (numpy.array or list) – -space vector
- sq (numpy.array or list) – vector
- r (numpy.array or list) – -space vector
Returns: Returns a tuple with and selected real space function
Return type: tuple of numpy.array
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static
apply_scales_and_offset
(x, y, dy=None, yscale=1.0, yoffset=0.0, xoffset=0.0)[source]¶ Applies scales to the Y-axis and offsets to both X and Y axes.
Parameters: - x (numpy.array or list) – X-axis data
- y (numpy.array or list) – Y-axis data
- yscale (float) – Y-axis scale factor
- yoffset (float) – Y-axis offset factor
- xoffset (float) – X-axis offset factor
Returns: X and Y vectors after scales and offsets applied
Return type: numpy.array pair
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bcoh_sqrd
¶ The average coherent scattering length, squared: = where the subscript implies for atom type , is the concentration of , is the coherent scattering length of , and is the complex coherent scattering length of
The real part of the term can be found from the Coh b column of the NIST neutron scattering length and cross section table found here: https://www.ncnr.nist.gov/resources/n-lengths/list.html
Units are in in the table for the term. Thus, has units of (and what PyStoG expects). NOTE: 100 == 1 .
Getter: Return the value of Setter: Set the value for Type: float
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btot_sqrd
¶ The average coherent scattering length, squared: = = where the subscript implies for atom type , is the concentration of and is the total cross-section of
The real part of the term can be found from the Scatt xs column of the NIST neutron scattering length and cross section table found here: https://www.ncnr.nist.gov/resources/n-lengths/list.html
Units are in (=100 ) in the table for the term. Thus, you must multiply by 100 to go from to (what PyStoG expects).
Getter: Return the value of Setter: Set the value for Type: float
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converter
= None¶ The converter attribute defines the Converter which is used to do all inner conversions necessary to go from the input reciprocal space functions, produce diagnostics for the selected real space functions, and finally output the desired real space function Must of type
pystog.converter.Converter
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density
¶ The number density used (atoms/) used for the term in the equations
Getter: Return the density value Setter: Set the density value Type: float
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dr
¶ The real space function X axis data, -space vector
Getter: Return the vector Setter: Set the vector Type: numpy.array
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extend_file_list
(new_files)[source]¶ Extend the file list with a list of new files
Parameters: new_files – List of new files Returns: File list extended by new_files Return type: list
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files
¶ The files that contain the reciprocal space data to merge together.
Getter: Current list of files to merge Setter: Set the list of files to merg Type: list
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filter
= None¶ The filter attribute defines the FourierFilter which is used to do all Fourier filtering if the fourier_filter_cutoff attribute is supplied. Must of type
pystog.fourier_filter.FourierFilter
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fourier_filter
()[source]¶ Performs the Fourier filter on the sq_master pattern to generate the desired real space function with this correction. The results from both reciprocal space and real space are:
- Saved back to the respective “master” dictionaries
- Saved to files via the stem_name
- Returned from function
Returns: Returns a tuple with , the selected real space function, , and functions Return type: tuple of numpy.array
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fourier_filter_cutoff
¶ This sets the cutoff in -space for the Fourier filter. The minimum is automatically 0.0. Thus, from 0.0 to fourier_filter_cutoff is reverse transfomed, subtracted in reciprocal space, and then the difference is back-transformed.
See
pystog.fourier_filter.FourierFilter
for more information.Getter: Return currently set cutoff value Setter: Set cutoff value Type: float
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fq_title
¶ The title of the function after merging and a fourier filter correction.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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gr_ft_title
¶ The title for the real space function after both merging and a fourier filter correction
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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gr_lorch_title
¶ The title for the real space function with the lorch correction
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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gr_master
¶ The “master” dictionary for the real space functions that are generated for each processing step.
Getter: Returns the current “master” real space functions dictionary generated up to the current step in the workflow. Setter: Sets the “master” real space function dictionary Type: dict[str:numpy.ndarray]
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gr_title
¶ The title of the real space function directly after merging the reciprocal space functions without any further corrections.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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lorch_flag
¶ This sets the option to perform the Lorch dampening correction for the range. Generally, will help reduce Fourier “ripples”, or AKA “Gibbs phenomenon”, due to discontinuity at if the reciprocal space function is not at the limit. Yet, will also broaden real space function peaks, possibly dubiously.
See
pystog.transformer.Transformer
fourier_transform and _low_x_correction methods for where this is applied.Getter: Return bool of applying the Lorch dampening correction Setter: Set whether the correction is applied or not Type: bool
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low_q_correction
¶ This sets the option to perform a low- correction for the omitted range.
See
pystog.transformer.Transformer
_low_x_correction method for more information.Getter: Return bool of applying the low- correction Setter: Set whether the correction is applied or not Type: bool
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merge_data
()[source]¶ Merges the reciprocal space data stored in the reciprocal_individuals numpy array into a single, merged recirocal space function. Stores the S(Q) result in sq_master dictionary using sq_title (default: “S(Q) Merged”).
Also, converts this merged into via the Converter class and applies any modification specified in merged_opts dict attribute, specified by the ‘Q[S(Q)-1]’ key of the dict. If there is modification, this modified will be converted to and replace the directly after merge.
Example dict of merged_opts for scaling of by 2 and then offsetting by 5:
{ "Merging": { "Y": { "Offset": 0.0, "Scale": 2.0 }, "Q[S(Q)-1]": { "Y": "Offset": 5.0, "Scale": 1.0 } } }
…
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merged_opts
¶ This sets the options to perform after merging the reciprocal space functions together, such as an overall offset and scale.
Getter: Return the options currently set Setter: Set the options for the merged pattern Type: dict
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q_master
¶ The “master” dictionary for the domain :math:Q` of the reciprocal space functions that are generated for each processing step.
Getter: Returns the current “master” reciprocal space functions dictionary generated up to the current step in the workflow. Setter: Sets the “master” dictionary Type: dict[str:numpy.ndarray]
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qmax
¶ The value to use for the Fourier transforms (from recirocal space -> real space). This overrides xmax attribute if qmax < xmax.
Getter: Returns the current set value Setter: Set the qmax value for the Fourier transforms Type: float
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qmin
¶ The value to use for the Fourier transforms (from recirocal space -> real space). This overrides xmin attribute if xmin < qmin.
Getter: Returns the current set value Setter: Set the value for the Fourier transforms Type: float
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qsq_minus_one_title
¶ The title of the function directly after merging the reciprocal space functions without any further corrections.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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r_master
¶ The “master” dictionary for the domain :math:r` of the real space functions that are generated for each processing step.
Getter: Returns the current “master” real space functions dictionary generated up to the current step in the workflow. Setter: Sets the “master” dictionary Type: dict[str:numpy.ndarray]
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rdelta
¶ The for the -space vector
Getter: Return value Setter: Set the value and update -space vector via the dr attribute Type: value
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read_all_data
(**kwargs)[source]¶ Reads all the data from the files attribute Uses the read_dataset method on each file.
Will append all datasets to the numpy storage array, reciprocal_individuals, and also convert to and add to the sq_individuals numpy storage array in add_dataset method via read_dataset method.
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read_dataset
(info, xcol=0, ycol=1, dycol=2, sep='\\s+', skiprows=2, **kwargs)[source]¶ Reads an individual file and uses the add_dataset method to apply all dataset manipulations, such as scales, offsets, cropping, etc.
Parameters: - info (dict) – Dict with information for dataset (filename, manipulations, etc.)
- xcol (int) – Column in data file for X-axis
- ycol (int) – Column in data file for Y-axis
- dycol (int) – Column in data file for Y uncertainty
- sep (raw string) – Separator for the file used by numpy.loadtxt
- skiprows (int) – Number of rows to skip. Passed to numpy.loadtxt
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read_nexus_file_by_bank
(nexus_file, bank, title, **kwargs)[source]¶ Reads an individual file bank by bank and uses the extract_xy to handle extraction and extract_path_from_title to obtain coord paths
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real_space_function
¶ The real space function to use throughoutt the processing
Getter: Returns the currently select real space function Setter: Set the selected real space function and updates other title attributes that rely on this in their name. Type: str
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reciprocal_individuals
¶ The storage array for the input reciprocal space functions loaded from files and with the loading processing from add_dataset class method.
Getter: Returns the current individual, input reciprocal space functions numpy array. The dimenions is where N is the number of patterns stored and M is the length of the patterns. Setter: Sets the numpy array Type: numpy.ndarray
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rmax
¶ The valuefor the -space vector
Getter: Return value Setter: Set the value and update -space vector via the dr attribute Type: value
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rmin
¶ The valuefor the -space vector
Getter: Return value Setter: Set the value and update -space vector via the dr attribute Type: value
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sq_ft_title
¶ The title of the function after merging and a fourier filter correction.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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sq_individuals
¶ The storage array for the generated from each input reciprocal space dataset in reciprocal_individuals array.
Getter: Returns the current individual reciprocal space functions numpy array. The dimenions is where N is the number of patterns stored and M is the length of the patterns. Setter: Sets the numpy array Type: numpy.ndarray
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sq_master
¶ The “master” dictionary for the reciprocal space functions that are generated for each processing step.
Getter: Returns the current “master” reciprocal space functions dictionary generated up to the current step in the workflow. Setter: Sets the “master” function dictionary Type: dict[str:numpy.ndarray]
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sq_title
¶ The title of the function directly after merging the reciprocal space functions without any further corrections.
Getter: Returns the current title for this function Setter: Sets the title for this function Type: str
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stem_name
¶ A stem name to prefix for all output files. Replicates the stog Fortran program behavior.
Getter: Return the currently set stem name Setter: Set the stem name for output files Type: str
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transform_merged
()[source]¶ Performs the Fourier transform on the merged sq_master pattern to generate the desired real space function with this correction. The results for real space are: the domain is saved to the r_master dictionary and the range is saved to the gr_master dictionary, with both using the gr_title for the key of the dictionaries.
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transformer
= None¶ The transformer attribute defines the Transformer which is used to do all Fourier transforms necessary from reciprocal space to real space and vice versa. Must of type
pystog.transformer. Transformer
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write_out_ft
(filename=None)[source]¶ Helper function for writing out the Fourier filter correction.
Parameters: filename (str) – Filename to write to
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write_out_ft_gr
(filename=None)[source]¶ Helper function for writing out the Fourier filtered real space function
Parameters: filename (str) – Filename to write to
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write_out_ft_sq
(filename=None)[source]¶ Helper function for writing out the Fourier filtered
Parameters: filename (str) – Filename to write to
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write_out_lorched_gr
(filename=None)[source]¶ Helper function for writing out the Lorch dampened real space function
Parameters: filename (str) – Filename to write to
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write_out_merged_gr
(filename=None)[source]¶ Helper function for writing out the merged real space function
Parameters: filename (str) – Filename to write to
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write_out_merged_sq
(filename=None)[source]¶ Helper function for writing out the merged
Parameters: filename (str) – Filename to write to
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write_out_rmc_fq
(filename=None)[source]¶ Helper function for writing out the output
Parameters: filename (str) – Filename to write to
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write_out_rmc_gr
(filename=None)[source]¶ Helper function for writing out the output
Parameters: filename (str) – Filename to write to
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xmax
¶ The maximum X value of all datasets to use for Fourier transforms (from recirocal space -> real space)
Getter: Returns the current set value Setter: Set the xmax value for the Fourier transforms Type: float
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xmin
¶ The minimum X value of all datasets to use for Fourier transforms (from recirocal space -> real space)
Getter: Returns the current set value Setter: Set the xmin value for the Fourier transforms Type: float
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