sxdm package¶

Submodules¶

sxdm.alignment module¶

sxdm.alignment.alignment_function(self)¶

Allows the user to align the scans based on Fluorescence or Region Of Interest.

Sets alignment variables and stores them in designated .h5 file. Easier to reload alignment data or redo alignment data

Parameters: self ((SXDMFrameset)) – the sxdmframeset object
Returns
Return type: Nothing

sxdm.alignment.reset_dxdy(self)¶

Resets the dxdy movements used for alignment of the frames

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: Nothing

sxdm.background module¶

sxdm.background.scan_background(self, amount2ave=3, multiplier=1)¶

Create background images for each scan.

Takes the first “amount2ave” and last “amount2ave” images of each scan and average them together to each scan. Create a dictionary of these background images.

Parameters

self ((SXDMFrameset)) –
amount2ave ((int)) – amount of images from the beginning and enf of each scan to average together
multiplier ((int/float)) – multiplier for each background scan

Returns

Return type

A dictionary of background images with entries for each scan number

sxdm.background.scan_background_finder(destination, background_dic)¶

The destination is the scan numbers associated with a given pixel location. This will take all scans in a pixel location and return a numpy array of their appropriate background images.

Parameters

destination ((numpy array)) – the output of h5get_image_destination(self, pixel) list of scan numbers which the user wants to get the background images for
background_dic ((dic)) – the dictionary otuput from the scan_background() function

Returns

Return type

A numpy array of background images corresponding to the scans in the destination input

sxdm.chi_determination module¶

class sxdm.chi_determination.Chi_FiguresClass¶

Bases: object

A class function that allows the code to store figure data. Makes it easier to transfer data between figures

sxdm.chi_determination.broadening_in_pixles(self)¶

Determine the instrumental broadening in pixels as well as the focal length and numberical aperature

Returns

Nothing
Sets
====
self.focal_length_mm
self.NA_mrads
self.broadening_in_pix

sxdm.chi_determination.chi_function(self)¶

Runs all code necessary to determine the chi bounds

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: Nothing

sxdm.chi_determination.chis(self)¶

Calculates the bounds for the detector

Parameters

(SXDMFrameset) (self) – the sxdmframeset

Returns

Nothing
Prints and Sets
======
self.chi value,
self.focal_length,
self.NA_mrads (numberical aperature),
self.broadening_in_pix of the detector

sxdm.chi_determination.closebtn_press(event, self, chi_figures)¶

Set the chi angle difference, position difference, and image dimension upon closing the figure

Parameters

(matplotlib event) (event) – matplotlib event
(SXDMFrameset) (self) – the SXDMFrameset)
(Chi_FiguresClass) (chi_figures) – the chi_figuresclass

Returns

Return type

Nothing - runs chis() function. see documentation for values set

sxdm.chi_determination.closebtn_start(chi_figures, btn_ax)¶

Set up the close button

Parameters

(Chi_FiguresClass) (chi_figures) – the chi_figuresclass
(matplotlib_axis) (btn_ax) – the figure axis corresponding to the close button

Returns

Return type

Nothing

sxdm.chi_determination.display_first_images(chi_figures)¶

From the chi figure class set up the first set of figures

Returns
Return type: Nothing

sxdm.chi_determination.display_second_images(chi_figures)¶

Display the second figure

Parameters: (Chi_FiguresClass) (chi_figures) – the chi_figuresclass
Returns
Return type: Nothing

sxdm.chi_determination.first_chi_figure_setup(self)¶

Setting up the chi figure GUI

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: The Chi_FigureClass object created by the function

sxdm.chi_determination.idx_tb_setup(vmin_spot_ax, vmax_spot_ax)¶

Set up the index textboxes DEPRECIATED

Returns
Return type: position 1 and position 2 textboxes for index values

sxdm.chi_determination.minmax_tb_setup(vmin_spot_ax, vmax_spot_ax)¶

Set up the minmax textboxes

Parameters

(matplotlib axis) (vmax_spot_ax) – the figure axis that corresponds to the vmin value of the spot diffraction
(matplotlib axis) – the figure axis that corresponds to the vmax value of the spot diffraction

Returns

Return type

vmin and vmax textboxes

sxdm.chi_determination.pos_tb_setup(pos1_ax, pos2_ax)¶

Set up the position text boxes

Parameters

(matplotlib axis) (pos2_ax) – the figure axis corresponding to the vertical line position of the first (left) image
(matplotlib axis) – the figure axis corresponding to the vertical line position of the second (right) image

Returns

Return type

position 1 and position 2 textboxes for index values

sxdm.chi_determination.return_chi_images(file, chi_figures)¶

Return the detector movement data

Parameters

(str) (file) – the file the user would like to find the detector images from
(Chi_FigureClass) (chi_figures) – the figure class. used to make it easier to move data around

Returns

Return type

Nothing - sets chi_fiures.images value

sxdm.chi_determination.return_chi_images_loc(file, chi_figures, detector_channel_loc='detector_channels/detector_scan/Main_Scan', zfill_num=4)¶

Grabs the image location for the detector sweep scan

Parameters

file ((str)) – the .h5 file associated with the dataset
chi_figures ((Chi_FigureClass)) – the Chi_FigureClass allowing transfer of data from figure to figure
detector_channel_loc ((str)) – the h5 group location to the detector sweep scan used for chi bounds determination
zfill_num ((int)) – the integer value for how many digits the scan number must have

Returns

Return type

Nothing - sets the chi_figures.scan_theta and chi_figures.images_location valuess

sxdm.chi_determination.second_change(event, chi_figures)¶

When the second figure values change, update the second figure

Parameters

(matplotlib event) (event) – matplotlib event
(Chi_FiguresClass) (chi_figures) – the chi_figuresclass

Returns

Return type

Nothing

sxdm.chi_determination.second_chi_figure_setup(chi_figures)¶

Setting up the second figure

Parameters: (Chi_FigureClass) (chi_figures) – the chi_figuresclass
Returns
Return type: Nothing

sxdm.chi_determination.vs_change(event, chi_figures)¶

When the user changes the vmin or vmax update the figures

Parameters

(matplotlib event) (event) – matplotlib event
(Chi_FiguresClass) (chi_figures) – the chi_figuresclass

Returns

Return type

Nothing

sxdm.clicks module¶

sxdm.clicks.check_mouse_ax(event, self)¶

Grabs the mouse axes position

Parameters

(matplotlib event) (event) – the matpotlib event
(SXDMFrameset) (self) – the sxdmframeset

Returns

Return type

Nothing - just checks which axis the mouse is in

sxdm.clicks.fig1_click(event, self, fig, images)¶

Deal with event clicks in the first figure and redraw plots

Parameters

(matplotlib event) (event) – matplotlib event
(SXDMFrameset) (self) – the sxdmframeset
(matplotlib figure) (fig) – the figure to be clicked on
(nd.array) (images) – the images to display

Returns

Return type

Nothing - deals with the clicks on the first image

sxdm.clicks.fig_leave(event, self)¶

If the user leaves an axis set the self.viewer_currentax to None :param event (matplotlib event): the matplotlib event :param self (SXDMFrameset): the sxdmframeset

Returns
Return type: Nothing

sxdm.clicks.onclick_1(event, self)¶

Deal with click events for first figure. Only allows for 30 figures

Once you click on figure one open up a second figure with the figure you just clicked on, but larger

Parameters

event ((matplotlib event)) – not 1100% sure. Needed to be the first param in a matplotlib event
self ((SXDMFrameset)) – An SXDMFrameset which allows the function to store click values

Returns

Return type

Nothing

sxdm.clicks.onclick_2(event, self)¶

Determine the pixel location the user has clicked on.

From the second figure that popped up, once you click on it, determine the location of that click

Parameters

(matplotlib event) (event) – Unsure. Needed to be the first variable in a matplotlib event click
(SXDMFrameset) (self) – An SXDMFrameset that allows the clicks to be saved

sxdm.clicks.save_alignment(event, self)¶

Allow the alignment click information to be saved to self.file

Parameters

(SXDMFrameset) (self) – the sxdmframeset object

Returns

Nothing. It just stores /dxdy to the self.file as well
as adding alingment_group and alignment_subgroup attributes

sxdm.det_chan module¶

sxdm.det_chan.add_column(im, max_column)¶

Add a numpy.nan column to an image array based on how many columns in the max amount of columns

Parameters

(a 2D array) (im) – the image array to add columns to
(int) (max_column) – the final amount of columns the user want to make the im array

Returns

Return type

a new im array with the User selected max_column

sxdm.det_chan.add_row(im, max_row)¶

Add a numpy.nan rows to an image array based on how many rows in the max amount of rows

Parameters

(a 2D array) (im) – the image array to add columns to
(int) (max_row) – the final amount of rows the user want to make the im array

Returns

Return type

a new im array with the User selected max_row

sxdm.det_chan.del_det_chan(file)¶

Deletes the /detector_channels group :param file (str): the .h5 file you would like to delete the detector_channel group from

Returns
Return type: Nothing

sxdm.det_chan.det_dim_fix(array, max_row, max_column)¶

Add columns and rows to image matrix to make everything the same dimensions

Parameters

(np.ndarray) (array) – a 3D array of images
(int) (max_column) – the max amount of rows the User would like to make all the images
(int) – the max amount of columns the User would like to make all the images

Returns

Return type

the 3D image array with dimensions (#images, max_row, max_column)

sxdm.det_chan.disp_det_chan(file)¶

Allows the user to quicky see what all values are set to in the detector_channel group

Parameters

(str) (file) – the .h5 file you would like to delete the detector_channel group from

Returns

prints the current values of the detector_channel group. If no values are currently set it displays something the
User can copy and paste into a cell to set the appropriate dectector values

sxdm.det_chan.max_dims(array)¶

Get the max dimensions for an array of 2D images

Parameters: (np.ndarray) (array) – a 3 dimensional array
Returns
Return type: the max rows and the max columns round for the 3 dimensionsal array

sxdm.det_chan.return_det(file, scan_numbers, group='fluor', default=False, dim_correction=True)¶

Returns all information for a given detector channel for an array of scan numbers

Parameters

file ((str)) – the .h5 file location
scan_numbers ((np.array)) – an array of scan numbers the user wants to get a specific detector channel information for
group ((str)) – a string corresponding to a group value that the user wants to return
default ((bool)) – If True this will default to the first acceptable detector_channel in the hdf5 file
dim_correction ((bool)) – If False this will not add rows and columns to the returned array to make them all the same shape

Returns

Return type

The specified detector channel for all specified scan numbers, the .mda detector value

sxdm.det_chan.setup_det_chan(file, fluor, roi, detector_scan, filenumber, sample_theta, hybrid_x, hybrid_y, mis, xrf)¶

Sets detector channel information and stores it in the .h5 file

Parameters

file ((str)) – the hdf file path
fluor ((dic)) – a dictionary entry with all the Fluorescence images names as well as their corresponding .mda detector channel vale
roi ((dic)) – a dictionary entry with all the Region of Interest images names as well as their corresponding .mda detector channel vale
detector_scan ((int)) – the dectector channel that corresponds to the scanning of the detector - used to determine detector dimensions
filenumber ((int)) – the dectector channel that corresponds to the image file numbers
sample_theta ((int)) – the detector channel that corresponds to the sample theta
hybrid_x ((int)) – the detector channel that corresponds to the hybrid_x
hybrid_y ((int)) – the detector channel that corresponds to the hybrid_y
mis ((dic)) – a miscellaneous dictionary with entries of detector channels that might be usefull. ex. 2Theta, Ring_Current
xrf ((dic)) – an x-ray fluorescence dictionary with entries of the detector channels CORRESPOND TO THE DETECTOR CHANNELS UNDER THE ‘xrf’ HEADING THE THE HDF FILE!!!

Returns

Return type

Nothing

sxdm.det_chan.space_check(fluor, roi, detector_scan, filenumber, sample_theta, hybrid_x, hybrid_y, mis, xrf)¶

Based on the input variables this checks to see if the user has put any spaces into their group names.

Warns the user that they are using spaces

Parameters

fluor ((dic)) – a dictionary entry with all the Fluorescence images names as well as their corresponding .mda detector channel value
roi ((dic)) – a dictionary entry with all the Region of Interest images names as well as their corresponding .mda detector channel vale
detector_scan ((int)) – the dectector channel that corresponds to the scanning of the detector - used to determine detector dimensions
filenumber ((int)) – the dectector channel that corresponds to the image file numbers
sample_theta ((int)) – the detector channel that corresponds to the sample theta
hybrid_x ((int)) – the detector channel that corresponds to the hybrid_x
hybrid_y ((int)) – the detector channel that corresponds to the hybrid_y
mis ((dic)) – a miscellaneous dictionary with entries of detector channels that might be usefull. ex. 2Theta, Ring_Current
xrf ((dic)) – an x-ray fluorescence dictionary with entries of the detector channels CORRESPOND TO THE DETECTOR CHANNELS UNDER THE ‘xrf’ HEADING THE THE HDF FILE!!!

Returns

Return type

(bool) on whether or not there is a space in any of the dictionary entries given by the user

sxdm.det_chan.true_filenumbers(file, scan_numbers, shapes)¶

Since the .mda files do not store the correct file_names/image_names inside of it. This creates an appropriate file number for each pixel in a scan

Parameters

(str) (file) – the location of the .h5 file
(nd.array) (shapes) – array of all the scan numbers the User wishes to create image numbers for
(nd.array) – the shapes of all the scans
Returns –
======= –
nd.array with the .tif image numbers/locations for each voxel of the scan (an) –

sxdm.generalize module¶

sxdm.generalize.general_analysis_multi(self, rows, columns, analysis_function, analysis_input, bkg_multiplier=0)¶

Runs the centroid analysis in a pool.map function

Parameters

self ((SXDMFrameset)) – the sxdmframeset object
rows ((int or tup)) – the total amount of rows the User wants to analyze or a tuple of the rows
columns ((int or tup)) – the total amount of columns the User wants to analyze or a tuple of the columns
med_blur_distance ((int)) – the median blur distance - must be odd
med_blur_height ((int)) – the median blur height
stdev ((int)) – the standard deviation used to segment data
bkg_multiplier ((int)) – the multiplier to the background images
analysis_function ((func)) – a function to be passed into the analysis. the program will find the summed diffraction pattern for each pixel, for each scan number of the dataset, background subtract, and pass the summed diffraction into the first analysis_function argument.
analysis_input ((user defined)) – an static input array, value, etc passed into the second argument in the analysis_function.

Returns

Return type

a pooled results from the centroid_pixel_analysis_multi() function

sxdm.generalize.general_pixel_analysis_multi(row, column, image_array, scan_numbers, background_dic, file, analysis_function, analysis_input)¶

The analysis done on a single pixel

Parameters

row ((int)) – the row the User wants to do analysis on
column ((int)) – the column the User wants to do analysis on
image_array ((nd.array)) – the image location array - can be created with create_imagearray(self)
scan_numbers ((nd.array)) – the list of scan numbers used
background_dic ((dic)) – the background scan dictionary entry - can be made with scan_backgrounnd(self)
file ((str)) – the hdf5 file location
analysis_function ((func)) – a function to be passed into the analysis. the program will find the summed diffraction pattern for each pixel, for each scan number of the dataset, background subtract, and pass the summed diffraction into the first analysis_function argument.
analysis_input ((user defined)) – an static input array, value, etc passed into the second argument in the analysis_function.

Returns

Return type

the analysis results as an nd.array

sxdm.generalize.general_pooled_return(results, user_val, user_acceptable_values)¶

Makes it easy to return values from the pooled results from the multi.analysis function

Parameters

(n dimensional array) (results) – the output from the analysis function
(str) (user_val) – a string that defines what the user wants to be returned. Type ‘help’ for all acceptable values
(list) (user_acceptable_values) – an array of all the analysis_function outputs in the order the user has set them as.

Returns

Return type

An n dimensional array consisting of the user selected data output from the multi.analysis function

sxdm.generalize.general_pre_multi(inputs, image_array, scan_numbers, background_dic, file, analysis_function, analysis_input)¶

Allows Python to run the roi analysis in a pool.map function

Parameters

inputs ((nd.array)) – the iterable inputs of rows and columns
image_array ((nd.array)) – the total locations of all the images - created by create_imagearray(self)
scan_numbers ((nd.array)) – the list of all the scan numbers
background_dic ((dic)) – the dictionary of all the background images - created by scan_background(self)
file ((str)) – the full hdf5 file location
analysis_function ((func)) – a function to be passed into the analysis. the program will find the summed diffraction pattern for each pixel, for each scan number of the dataset, background subtract, and pass the summed diffraction into the first analysis_function argument.
analysis_input ((user defined)) – an static input array, value, etc passed into the second argument in the analysis_function.

Returns

Return type

the results from the general_pixel_analysis_multi() function

sxdm.h5 module¶

sxdm.h5.close_h5(hdf)¶

Closing and opened hdf5 file

Parameters: (str) (file) – the path to the hdf5 file
Returns
Return type: Closes an opened hdf5 file

sxdm.h5.h5create_dataset(file, ds_path, ds_data)¶

Creates a dataset in the user defined group with data equal to the user defined data

Parameters

file ((str)) – the user defined hdf5 file
ds_path ((str)) – the group path to the dataset inside the hdf5 file
ds_data ((nd.array)) – a numpy array the user would like to store

Returns

Return type

Nothing

sxdm.h5.h5create_file(loc, name)¶

Creates hdf5 file

Parameters

loc ((str)) – the location of the hdf5 file
name ((str)) – the name of the hdf5 file WITHOUT .h5 at the end

Returns

Return type

Nothing

sxdm.h5.h5create_group(file, group)¶

Creates a group based on the Users group input

Parameters

(str) (group) – the user defined hdf5 file
(str) – the group the user would like to create inside the file

Returns

Return type

Nothing

sxdm.h5.h5del_data(file, group)¶

Sets all data equal to zero for a given dataset.

Parameters

file ((str)) – the hdf5 file path
group ((str)) – the group location in the hdf5 the user wants to delete the data for

Returns

Return type

Nothing

sxdm.h5.h5del_group(file, group)¶

Deletes the user defined group. DOES NOT REDUCE FILE SIZE

Parameters

file ((str)) – the user defined hdf5 file
group ((str)) – the group inside the hdf5 file the user would like to delete

Returns

Return type

Nothing

sxdm.h5.h5delete_file(file)¶

Deletes the file set by the user

Parameters: file ((str)) – the full location of the hdf5 file the user would like to delete
Returns
Return type: Nothing

sxdm.h5.h5get_image_destination(self, pixel)¶

Determine where all the .tif images are for all the scan numbers disregarding the nan values

Parameters

(SXDMFramset) (self) – the sxdmframset
(str array) (pixel) – the image number from each scan that corresponds to a certain pixel

Returns

Return type

All of the diffraction FULL image locations for each scan in a 3D array - excluding the np.nan’s

sxdm.h5.h5get_image_destination_v2(self, pixel)¶

Determine where all the .tif images are for all the scan numbers disregarding the nan values

Parameters

(SXDMFramset) (self) – the sxdmframset
(str array) (pixel) – the image number from each scan that corresponds to a certain pixel

Returns

Return type

All of the diffraction FULL image locations for each scan in a 3D array - excluding the np.nan’s

sxdm.h5.h5grab_data(file, data_loc)¶

Returns the data stored in the user defined group

Parameters

(str) (data_loc) – the user defined hdf5 file
(str) – the group the user would like to pull data from

Returns

Return type

the data stored int the user defined location

sxdm.h5.h5group_list(file, group_name='base')¶

Displays all group members for a user defined group

Parameters

(str) (group_name) – the path to the hdf5 file
(str) – the path to the group the user wants the Keys for. Set to ‘base’ if you want the top most group

Returns

Return type

a list of all the subgroups inside the user defined group

sxdm.h5.h5images_wra(file, scan, im_loc, im_name, delete=False, import_type='uint32')¶

Used to import/delete .tif images into the .h5 file

Parameters

(str) (import_type) – the user defined hdf5 file
(nd.array) (scan) – the scan numbers the user wants to import
(str) – the location of the image file
(bool) (delete) – set to True if the user would like to delete the data in the hdf5 file
(str) – string passed into imageio.imread(image).astype(import_type)

Returns

Return type

Nothing

sxdm.h5.h5path_exists(file, loc)¶

See if the group the user selected exists

Parameters

(str) (loc) – the path to the hdf5 file
(str) – the location to the group the user wishes to check the status of

Returns

Return type

a bool (True or False) on whether or not the group exists

sxdm.h5.h5read_attr(file, loc, attribute_name)¶

Read an attribute from a user selected group and attribute name

Parameters

(str) (attribute_name) – the path to the hdf5 file
(str) – the location to the group inside the hdf5 file
(str) – the name of the attribute

Returns

Return type

Attribute value

sxdm.h5.h5replace_data(file, group, data)¶

Replaces all data in a dataset.

Helps with space savings since deleting groups does not decrease the file size. Easier to replace data

Parameters

(str) (group) – the user defined hdf5 file
(str) – the user defined group in the hdf5 file
(nd.array) (data) – the data the user would like to sub in

Returns

Return type

Nothing

sxdm.h5.h5set_attr(file, loc, attribute_name, attribute_val)¶

Set and attribute for a User selected group

Parameters

(str) (attribute_name) – the path to the hdf5 file
(str) – the group location in the hdf5 file
(str) – the name the user wants to set the attribute value of
(str or int) (attribute_val) – the value of the attribute

Returns

Return type

Nothing

sxdm.h5.open_h5(file)¶

Opening an hdf5 file

Parameters: (str) (file) – the path to the hdf5 file
Returns
Return type: The opened hdf5 file

sxdm.importer module¶

sxdm.importer.images_group_exsist(file, scan)¶: See if the images group exists.

sxdm.importer.import_images(file, images_loc, scans=False, fill_num=4, import_type='uint32', delimiter_function=<function delimiter_func>, force_reimport=False)¶

Allows the user to import all .tif images into the .h5 file

Parameters

(str) (import_type) – the user defined hdf5 file
(str) – the location of the images folder from the beamline
(nd.array) (scans) – the scans the user would like to import
(int) (fill_num) – the amount of numbers in the images folders names
(str) – a string value passed into imageio.imread().astype(import_type)
(function) (delimiter_function) – a function which determines the image number. redefine this if 26 - ID -C naming scheme changes
(bool) (force_reimport) – set to True if you would like to force reimport images

Returns

Return type

Nothing

sxdm.importer.import_mda(mda_path, hdf5_save_directory, hdf5_save_filename, single_file=False, maxdims=2)¶

Allows the User to import all .mda image and line scan data into an hdf5 format

Parameters

(str) (single_file) – the string path to the folder holding the .mda files
(str) – the path location where you would like to save your data to EXAMPLE: ‘/home/Desktop’
(str) – the file inside that path in which you would like to save data to (DO NOT INCLUDE “.h5”) EXAMPLE: ‘test’
(str) – the location of the file to import
(int) (maxdims) – the maximum dimensions for the readMDA function to import from the .mda file

Returns

Return type

Nothing - Will Not Reimport Files

sxdm.logger module¶

sxdm.logger.initialize_logging(self)¶

Initiate logging

Not set up

sxdm.mis module¶

sxdm.mis.array2dic(array)¶

Turn a numpy array into a dictionary

Parameters: (numpy array) (array) – a numpy array of form [(num1, num2), (num3, num4)] that will be turned into a dictionary
Returns: a dictionary of form {0
Return type: (num1, num2), 1: (num3, num4)``}``

sxdm.mis.array_shift(self, arrays2shift, centering_idx)¶

Translate a 3D stack of numpy arrays to align based on set centering values

Parameters

(SXDMFrameset) (self) – the sxdmframeset
(numpy array) (centering_idx) – the 3 dimensional array the user wants to center around one of the indexes
(numpy array) – the dxdy values (translation values) for each matrix in the array

Returns

Return type

the shifted array based on the dxdy values

sxdm.mis.centering_det(self, group='fluor', center_around=False, summed=False, default=False)¶

Return a detector that has been centered around a set value

Parameters

(SXDMFrameset) (self) – the sxdmframeset
(str) (group) – the group name the user would like to center to - acc_vals = fluor and roi
(bool) (default) – if this equals -1 then there will be no centering adjustments
(bool) – if True it will sum together all scans after centering
(bool) – if True it will set the fluor image to center on or roi image to view to the first index

Returns

an array of the fluor images or the roi images for all the SXDMFrameset scans centered around
the users value

sxdm.mis.create_file(file)¶

Create an hdf5 file

Parameters: (str) (file) – the path of the hdf5 file the user would like to create
Returns
Return type: Nothing

sxdm.mis.create_rois(self)¶

Take the self.roi_results and make them into something more useful

Parameters

(SXDMFrameset) (self) – the sxdmframset

Returns

the region of interst maps for each scan, the region of interest maps for the user defined
sub regions of interest

sxdm.mis.delimiter_func(string)¶

The delimiter function used in the image importer Used to just get the number of the image from the name of the image/mda file

Parameters: (str) (string) – the string the user wants to place the delimiter function on
Returns
Return type: a cropped string based on the delimiter function

sxdm.mis.dic2array(dic)¶

Turn a dictionary into a numpy array

Parameters: (dictionary) (dic) – a dictionary of form {0: (num1, num2), 1: (num3, num4)}
Returns
Return type: a numpy array of form [(num1, num2), (num3, num4)]

sxdm.mis.figure_size_finder(images)¶

Determines the amount of boxes to place in the alignment viewer

Parameters: (nd.array) (images) – the numpy array
Returns
Return type: the amount of images to make axes for in plt.subplot((return, return))

sxdm.mis.get_idx4roi(pix, destination, scan_numbers)¶

Based on the pixel being loaded, this returns the index of each scan used in the self.scan_numbers

Parameters

(array of strings) (scan_numbers) – the image numbers for each scan for a given pixel
(array of strings) – full diffraction image locations for each scan for a given pixel
(array of strings) – the self.scan_numbers value

Returns

Return type

an array of index values for a master roi used to store values in the correct position

sxdm.mis.grab_dxdy(self)¶

Return the dxdy movements for each scan

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: the dxdy values stored in the self.file

sxdm.mis.grab_fov_dimensions(self)¶

Returns the image dimensions for the User

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: the np.shape() of the fluorescence images - which are identical for the the entire field of view

sxdm.mis.image_numbers(self)¶

Grab the image numbers

Parameters: (SXDMFrameset) (self) – the sxdmframset
Returns
Return type: all of the diffraction image numbers for each scan in a 3D matrix

sxdm.mis.load_variable_pickle(file)¶

sxdm.mis.median_blur_numpy(input_array, median_blur_distance, cut_off_value_above_mean, with_low=False)¶

Median Blur a 1D array. Used for eliminating hot or dead pixels

Parameters

(1D array) (input_array) – a one dimensional numpy array
(int) (median_blur_distance) – the chunk size of numbers to to check for a median blur corrections

Returns

Return type

a 1 dimensional numpy array that has been median blurred

sxdm.mis.median_blur_selective(input_array, median_blur_distance, cut_off_value_above_mean, with_low=False)¶

Allows for the user to have a selective median blur for individual spots. Meaning it will not assign a median blur to the entire spectra.

Parameters

(nd.array) (input_array) – the 1D spectral array
(int) (cut_off_value_above_mean) – a value that assigns how large of a median blur the User wants to walk through.
(int) – a value above the mean value for the med_blur_distance in which the value gets attributed as the median of that data chunk
(bool) (with_low) – True median blurs on values way above or way below the mean. Rather than just way above.

Returns

Return type

An 1D spectral array with appropriate values median blurred

sxdm.mis.order_dir(path)¶

For a selected path return the ordered filenames. Meant for ordering images inside of a folder

Parameters: (str) (path) – the path to the folder you would like to order the contents of
Returns
Return type: the full image location, image name

sxdm.mis.ram_check()¶

Check how much RAM is being used. If it’s over 90% then the analysis function stop loading information

Returns
Return type: the percent of RAM usage

sxdm.mis.resolution_check(self, user_resolution_um=0.0005)¶

Check if all X dimensions for all scans are equal to each other. Also checks in all y dimensions for all scans are equal to each other. Then checks if the x and y are equal to one another.

Parameters

(SXDMFramset) (self) – the sxdmframset
(float) (user_resolution_um) – the resolution in um the user would like the scan dimensions for

Returns

Return type

Nothing - sets resolution values

sxdm.mis.results_2dsum(self)¶

Returns the 2d summed diffraction pattern from the results self.saved_file without loading all the diffraction data. This works on the self.results variable.

Problems - Uses a lot of RAM

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: 2d image array of the summed diffraction pattern

sxdm.mis.save_variable_pickle(array_of_vars, file)¶

sxdm.mis.scan_num_convert(scan_numbers, fill_num=4)¶

Convert the users int scan numbers into strings

Parameters

(str or int) (scan_numbers) – takes an array of str values or int values and zfills them accordingly
(int) (fill_num) – the string fill number the user would like to use

Returns

Return type

the scan numbers in an array of strings with the user selected fill number

sxdm.mis.set_centering(self)¶

Set the centering values for each scan

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: The centering index - sets all centering data

sxdm.mis.shape_check(self)¶

Check to see if the imported hybrids have the same shape

Parameters: (SXDMFrameset) (self) – the sxdmframeset used
Returns
Return type: Nothing. Prints Important Data

sxdm.mis.show_hybrid_dimensions(self)¶

Shows the hybrid x and hybrid y image dimensions

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: prints the hybrid x an y dimensions

sxdm.mis.tif_separation(string, func=<function delimiter_func>)¶

Separating the image number from the full name stored in the images folder through the user of the delimiter_func

Parameters

(str) (string) – the string the user wants to place the delimiter function on
(function) (func) – the delimiter function for the string. Makes it easier to change in later versions

Returns

Return type

the image string name of just the number

sxdm.mis.total_rows_int_tup(input, difference=False)¶

Allows the user to return the true starting and ending values for a scan. Useful for when scans do not start at zero.

Parameters

(int or tuple) (input) – the int or tuple input of the analysis functions
(bool) (difference) – if the User would like to take the difference between the starting and ending points

Returns

Return type

Either the starting and ending values for a scan or the difference between them

sxdm.mis.val_check(array, resolution)¶

Check the resolution of the x and y dimensions of the scans

Parameters

(nd.array) (array) – array of all the scan x or y dimensions
(float) (resolution) – a numbers in microns that sets the resolution check of the x and y dimensions

Returns

Return type

bool (True or False) on whether or not the scan dimensions are within the set resolution

sxdm.mis.zfill_scan(scan_list, fill_num)¶

Change int to str and fill them with the user set number of zeros

Parameters

(str) (scan_list) – a list string of the scans the user would like to import
(int) (fill_num) – the amount of numbers each number should have. fill_num=4 turns ‘40’ into ‘0040’

Returns

Return type

A list of scan numbers with corrected zfill values

sxdm.multi module¶

sxdm.multi.centroid_map_analysis(self, rows, columns, med_blur_distance=4, med_blur_height=10, stdev_min=35, multiplier=1, center_around=False)¶

Calculates spot diffraction and data needed to make 2theta/chi/roi maps

Parameters

self ((SXDMFramset)) – the sxdmframset
rows ((int)) – the total number of rows you want to iterate through
columns ((int)) – the total number of columns you want to iterate through
med_blur_distance ((int)) – the amount of values to scan for median blur
med_blur_height – (int) the height cut off for the median blur
stdev_min ((int)) – standard deviation above the mean of signal to ignore
multiplier ((int)) – multiplier for the background signal to be subtracted
center_around ((int)) – the index of the scan you would like to center around

Returns

A numpy matrix of every pixel asked. Each pixel contains
row_column,(row, column), summed_dif, ttheta, chi,
ttheta_centroid_finder, ttheta_centroid,
chi_centroid_finder, chi_centroid, full_roi

sxdm.multi.create_imagearray(self, center_around=False)¶

Creates the self.image_array variable needed for pixel_analysis

Parameters

(SXDMFrameset) (self) – the sxdmframset
(bool) (center_around) – setting this to True allows the user to default to the first image index to center around

Returns

Return type

Nothing - sets the self.image_array value

sxdm.multi.initialize_vectorize(num_rows, num_columns)¶

Places the row and column number next to each other in an iterable array.: Used for starmap multiprocessing pixels.

Parameters

num_rows ((int)) – Total number of rows the user wants to calculate
num_columns ((int)) – Total number of columns the user wants to calculate

Returns

Return type

An iterable array of pixel locations to be passed into the multiprocessing pixel analysis

sxdm.multi.iterations(self, num_rows, num_columns)¶

Places the row and column number next to each other in an iterable array.: Used for starmap multiprocessing pixels.

Parameters

self ((SXDMFrameset)) –
num_rows ((int)) – Total number of rows the user wants to calculate
num_columns ((int)) – Total number of columns the user wants to calculate

Returns

Return type

An iterable array of pixel locations to be passed into the multiprocessing pixel analysis

sxdm.multi.pooled_return(results, user_val)¶

Makes it easy to return values from the pooled results from the multi.analysis function

Parameters

(n dimensional array) (results) – the output from the analysis function
(str) (user_val) – a string that defines what the user wants to be returned

Returns

Return type

An n dimensional array consisting of the user selected data output from the multi.analysis function

sxdm.multi.roi_analysis(self, rows, columns, med_blur_distance=4, med_blur_height=10, stdev_min=35, multiplier=1, center_around=False, diff_segmentation=True)¶

Calculates region of interest for each scan as well as the region of interest maps for user defined sub region of interests

Parameters

self ((SXDMFramset)) – the sxdmframset
rows ((int)) – the total number of rows you want to iterate through
columns ((int)) – the total number of columns you want to iterate through
med_blur_distance ((int)) – the amount of values to scan for median blur
med_blur_height – (int) the height cut off for the median blur
stdev_min ((int)) – standard deviation above the mean of signal to ignore
multiplier ((int)) – multiplier for the background signal to be subtracted
center_around ((int)) – the index of the scan you would like to center around
diff_segmentation ((bool)) – if set to True this will initiate the user sub region of interest analysis

Returns

A numpy matrix of every pixel asked. Each pixel contains
[(row, column), idxs, – raw_scan_data, corr_scan_data, scan_data_roi_vals, summed_data, corr_summed_data, summed_data_roi_vals]

sxdm.multi_update module¶

sxdm.multi_update.centroid_analysis_multi(self, rows, columns, med_blur_distance=9, med_blur_height=100, stdev=35, bkg_multiplier=0)¶

Runs the centroid analysis in a pool.map function

Parameters

self ((SXDMFrameset)) – the sxdmframeset object
rows ((int or tup)) – the total amount of rows the User wants to analyze or a tuple of the rows
columns ((int or tup)) – the total amount of columns the User wants to analyze or a tuple of the columns
med_blur_distance ((int)) – the median blur distance - must be odd
med_blur_height ((int)) – the median blur height
stdev ((int)) – the standard deviation used to segment data
bkg_multiplier ((int)) – the multiplier to the background images

Returns

Return type

a pooled results from the centroid_pixel_analysis_multi() function

sxdm.multi_update.centroid_pixel_analysis_multi(row, column, median_blur_distance, median_blur_height, stdev_min, image_array, scan_numbers, background_dic, file)¶

The analysis done on a single pixel :param row: the row the User wants to do analysis on :type row: (int) :param column: the column the User wants to do analysis on :type column: (int) :param median_blur_distance: the amount of values to scan for median blur :type median_blur_distance: (int) :param median_blur_height: the height cut off for the median blur :type median_blur_height: (int) :param stdev_min: standard deviation above the mean of signal to ignore :type stdev_min: (int) :param image_array: the image location array - can be created with create_imagearray(self) :type image_array: (nd.array) :param scan_numbers: the list of scan numbers used :type scan_numbers: (nd.array) :param background_dic: the background scan dictionary entry - can be made with scan_backgrounnd(self) :type background_dic: (dic) :param file: the hdf5 file location :type file: (str)

Returns
Return type: the analysis results as an nd.array

sxdm.multi_update.centroid_pre_analysis(inputs, meds_d, meds_h, st, image_array, scan_numbers, background_dic, file)¶

Allows Python to run the centroid analysis in a pool.map function

Parameters

inputs ((nd.array)) – the iterable inputs of rows and columns
meds_d ((int)) – the median blur distance value
meds_h ((int)) – the median_blur height value
image_array ((nd.array)) – the total locations of all the images - created by create_imagearray(self)
scan_numbers ((nd.array)) – the list of all the scan numbers
background_dic ((dic)) – the dictionary of all the background images - created by scan_background(self)
file ((str)) – the full hdf5 file location
diff_segments ((bool)) – if True this will run the segmentation analysis as well

Returns

Return type

the results from the centroid_pixel_analysis_multi() function

sxdm.multi_update.h5get_image_destination_multi(scan_numbers, pixel)¶

Determine where all the .tif images are for all the scan numbers disregarding the nan values

Parameters

(nd.array) (scan_numbers) – the scan numbers the user wants to get
(str array) (pixel) – the image number from each scan that corresponds to a certain pixel

Returns

Return type

All of the diffraction FULL image locations for each scan in a 3D array - excluding the np.nan’s

sxdm.multi_update.roi_analysis_multi(self, rows, columns, med_blur_distance=9, med_blur_height=100, bkg_multiplier=0, diff_segments=True)¶

Runs the region of interest analysis in a pool.map function

Parameters

self ((SXDMFrameset)) – the sxdmframeset object
rows ((int or tup)) – the total amount of rows the User wants to analyze or a tuple of the rows
columns ((int or tup)) – the total amount of columns the User wants to analyze or a tuple of the columns
med_blur_distance ((int)) – the median blur distance - must be odd
med_blur_height ((int)) – the median blur height
bkg_multiplier ((int)) – the multiplier to the background images
diff_segments ((bool)) – if True this will analyze the roi segmentations

Returns

Return type

a pooled results from the roi_pixel_analysis_multi() function

sxdm.multi_update.roi_pixel_analysis_multi(row, column, median_blur_distance, median_blur_height, image_array, scan_numbers, background_dic, file, diff_segments=False)¶

The analysis done on a single pixel - this will get the new roi for each theta and be able to segment out diffraction areas and create the roi for them :param row: the total number of rows you want to iterate through :type row: (int) :param column: the total number of columns you want to iterate through :type column: (int) :param median_blur_distance: the amount of values to scan for median blur :type median_blur_distance: (int) :param median_blur_height: the height cut off for the median blur :type median_blur_height: (int) :param image_array: the location for all the pixels - can be created through create_imagearray(self) :type image_array: (nd.array) :param scan_numbers: the list of scan numbers :type scan_numbers: (array) :param background_dic: the dictionary for the background images - created through scan_background(self) :type background_dic: (dic) :param file: the location to the hdf5 file :type file: (str) :param diff_segments: array used for segmenting the diffraction patterns :type diff_segments: (array)

Returns

the analysis results as an nd.array
[(row, column), idxs, – raw_scan_data, corr_scan_data, scan_data_roi_vals, summed_data, corr_summed_data, summed_data_roi_vals]

sxdm.multi_update.roi_pre_analysis(inputs, meds_d, meds_h, image_array, scan_numbers, background_dic, file, diff_segments)¶

Allows Python to run the roi analysis in a pool.map function

Parameters

inputs ((nd.array)) – the iterable inputs of rows and columns
meds_d ((int)) – the median blur distance value
meds_h ((int)) – the median_blur height value
image_array ((nd.array)) – the total locations of all the images - created by create_imagearray(self)
scan_numbers ((nd.array)) – the list of all the scan numbers
background_dic ((dic)) – the dictionary of all the background images - created by scan_background(self)
file ((str)) – the full hdf5 file location
diff_segments ((bool)) – if True this will run the segmentation analysis as well

Returns

Return type

the results from the roi_pixel_analysis_multi() function

sxdm.multi_update.sum_pixel_multi(file, images_loc)¶

Sum a pixel :param file (str): the full file location of the hdf5 file :param image_loc (list of str): the full image location in the hdf5 file

Returns
Return type: all images set in the image_loc variable

sxdm.pixel module¶

sxdm.pixel.centroid_finder(oneDarray_start, stdev_min=35)¶

Determine the centroid function :param oneDarray_start (numpy array): a one dimensions numpy array :param stdev_min (int): the standard deviation minimum the user would like to section the data off with

Returns
Return type: the corrected one dimensional array and the centroid of the array

sxdm.pixel.centroid_pixel_analysis(self, row, column, median_blur_distance, median_blur_height, stdev_min)¶

The analysis done on a single pixel :param self (SXDMFrameset): the sxdmframset :param rows: the total number of rows you want to iterate through :type rows: (int) :param columns: the total number of columns you want to iterate through :type columns: (int) :param med_blur_distance: the amount of values to scan for median blur :type med_blur_distance: (int) :param med_blur_height: the height cut off for the median blur :type med_blur_height: (int) :param stdev_min: standard deviation above the mean of signal to ignore :type stdev_min: (int) :param bkg_multiplier: multiplier for the background signal to be subtracted :type bkg_multiplier: (int)

Returns

the analysis results as an nd.array
# For a given row and column
[
(row_index, column_index),
summed diffraction pattern (set to zero to save RAM. User can change in source code in /pixel.py),
two theta centroid value (float)
chi centroid value (float)
two theta cropped signal (nd.array)
full two theta signal (nd.array)
chi cropped signal (nd.array)
full chi signal (nd.array)
summed region of interest value (float)
]

sxdm.pixel.chi_maths(summed_dif, median_blur_distance, median_blur_height, stdev_min, q=False)¶

Determine the centroid of the chi axis :param summed_dif (nd.array image): a 2D summed diffraction image :param median_blur_distance (int): the amount of values to take the median of :param median_blur_height (int): the value above the median to replace with the median value :param stdev_min (int): the standard deviation above the noise to consider the signal valid :param q (bool): used for an old multi processing function - unused now - might be put in at a later date

Returns

the edited (median blured) sum down the x axis
the centroid of the data
the cropped data to find the centroid
the edited (median blured) sum down the x axis as a numpy array

sxdm.pixel.grab_pix(array, row, column, int_convert=False)¶

Return a pixel at a given row and column value :param array (nd.array): a 3 dimensional numpy array :param row (int): the row the user would like to grab :param column (int): the column the user would like to grab :param int_convert (bool): if the user would like to change np.nans to integers set this to True

Returns
Return type: All data associated with the set row and column for the 3 dimensional array

sxdm.pixel.pixel_diffraction_grab(self, image_array, row, column)¶

Returns the diffraction image for a specific scan location (row, column)

Parameters

self ((SXDMFrameset object)) – the sxdmframset object
image_array ((nd.array)) – the array that holds all the diffraction image locations self.im_array()
row ((int)) – the row the User would like to return data for
column ((int)) – the column the User would like to return data for

Returns

Return type

Summed diffraction image for a single pixel

sxdm.pixel.roi_pixel_analysis(self, row, column, median_blur_distance, median_blur_height, diff_segments=False)¶

The analysis done on a single pixel - this will get the new roi for each theta and be able to segment out diffraction areas and create the roi for them :param self (SXDMFrameset): the sxdmframset :param rows: the total number of rows you want to iterate through :type rows: (int) :param columns: the total number of columns you want to iterate through :type columns: (int) :param med_blur_distance: the amount of values to scan for median blur :type med_blur_distance: (int) :param med_blur_height: the height cut off for the median blur :type med_blur_height: (int) :param diff_segments: array used for segmenting the diffraction patterns :type diff_segments: (array)

Returns

the analysis results as an nd.array
[(row, column), idxs, – raw_scan_data, corr_scan_data, scan_data_roi_vals, summed_data, corr_summed_data, summed_data_roi_vals]

sxdm.pixel.segment_diffraction_roi(diffraction)¶

Creates a roi value and the raw data analysis for the ROI maps

Parameters: (image) (diffraction) – the summed diffraction image
Returns
Return type: ttheta, ttheta_copy, np.sum(ttheta_copy), scan_roi_val

sxdm.pixel.sum_pixel(self, images_loc)¶

Sum a pixel :param self (SXDMFrameset): the sxdmframset :param image_loc (list of str): the full image location in the hdf5 file

Returns
Return type: all images set in the image_loc variable

sxdm.pixel.sum_pixel_v2(images_loc, file)¶

Sum a pixel :param image_loc (list of str): the full image location in the hdf5 file :param file: the opened hdf file :type file: (hdf file)

Returns
Return type: all images set in the image_loc variable

sxdm.pixel.theta_maths(summed_dif, median_blur_distance, median_blur_height, stdev_min, q=False)¶

Determine the centroid of the theta axis :param summed_dif (nd.array image): a 2D summed diffraction image :param median_blur_distance (int): the amount of values to take the median of :param median_blur_height (int): the value above the median to replace with the median value :param stdev_min (int): the standard deviation above the noise to consider the signal valid :param q (bool): used for an old multi processing function - unused now - might be put in at a later date

Returns

the edited (median blured) sum down the y axis
the centroid of the data
the cropped data to find the centroid
the edited (median blured) sum down the y axis as a numpy array

sxdm.postprocess module¶

sxdm.postprocess.centroid_roi_map(results, map_type='chi_centroid')¶

Returns the centroid or roi based on the Centroid Analysis :param results (nd.array): self.results or the output of self.analysis :param map_type (str): the value the user would like to return acceptable values are chi_centroid, ttheta_centroid, or full_roi

Returns
Return type: the user selected map in an nd.array

sxdm.postprocess.maps_correct(user_map, new_bounds)¶

Takes the centroid_rou_map() function output and gives it new bounds :param user_map (nd.array): the output of the centroid_roi_map function :param new_bounds (np.linspace): np.linspace(lowerbound, higherbound, dim of image)

Returns

nd.array of the user_map, but with new bounds rather than with the dimensions
of the diffraction image

sxdm.postprocess.pixel_analysis_return(results, row, column, show_accep_vals=False)¶

Easy return of the results based on the input row and column value :param results (nd.array): self.results or output of self.analysis :param row (int): the row the user would like to look at :param column (int): the column the user would like to look at

Returns

A dictionary with entries
’row_column’,
’summed_dif’,
’ttheta’,
’chi’,
’ttheta_corr’,
’chi_corr’,
’ttheta_cent’,
’chi_cent’,
’roi’

sxdm.postprocess.saved_return(file, group, summed_dif_return=False)¶

Load saved data :param file (str): a user defined hdf5 file :param group (str): the group the user would like to import :param summed_dif_return (bool): if True this will import all data. it is set to False because this import take up a lot of RAM

Returns
Return type: a nd.array thay can be set to the self.results value

sxdm.postprocess.twodsummed(results)¶

Returns the summed diffraction pattern for the analysis output :param results (nd.array): the self.results or output of self.analysis

Returns
Return type: the summed diffraction patter from the analysis output

sxdm.preprocess module¶

sxdm.preprocess.gaus_check(self, center_around=False, default=False)¶

Determines the intensity change over all group scans

Parameters

(SXDMFrameset) (self) – the sxdmframset

Returns

the x and y values for a plot that shows intensity vs scan angle.
also auto displays the figure

sxdm.preprocess.init_dxdy(self)¶

Initializes a group that scan store dxdy data

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: Nothing - creates a blank self.dxdy_store variable

sxdm.preprocess.initialize_experimental_attrs(self)¶

Initialized the Kev and detector’s theta position.

Sets attributes of Kev and detector theta position to the current user defined group

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: Nothing - sets Kev and detector_theta attributes

sxdm.preprocess.initialize_group(self)¶

Initialized the group assigned by the user to the user defined file.

From the scan numbers the program determines the scan_theta as well checking if identical settings have already been imported. If so the program reloads saved settings

Parameters: (SXDMFrameset) (self) – the sxdmframeset
Returns
Return type: Nothing - sets /scan_numbers and /scan_theta

sxdm.preprocess.initialize_saving(self)¶

Initialize the ability to save data

Parameters: (SXDMFrameset) (self) – the sxdmframset
Returns
Return type: Nothing - creates the filename_savedata.h5 file to save data to

sxdm.preprocess.initialize_scans(self, scan_numbers=False, fill_num=4)¶

Initialize all necessities for each scan

Parameters

(SXDMFrameset) (self) – the sxdmframeset
(nd.array of int) (scan_numbers) – the list of scan numbers the user wants to create [178, 178, …]
(int) (fill_num) – the zfill number for the scan number integers

Returns

Return type

Nothing - sets self.scan_numbers, self.det_smpl_theta, and self.scan_theta

sxdm.preprocess.initialize_zoneplate_data(self, reset=False)¶

Initialize values for the zoneplate used as well as detector pixel size.

Asks the user what the parameters of the zone plate are and detector pixel size. If they have been already set then the program displays the current values when setting up SXDMFrameset object

Parameters

(SXDMFrameset) (self) – the sxdmframset
(bool) (reset) – if True this allows the user to reset all values

Returns

Return type

Nothing - sets values inside /zone_plate/

sxdm.preprocess.max_det_val(self, detector='fluor')¶

Used to determine the max values for a given detector channel

Parameters

(SXDMFrameset) (self) – the sxdmframeset
(str) (detector) – value to be passed into the return_det() function

Returns

Return type

the max values for all scans for a given detector channel input

sxdm.roi module¶

sxdm.roi.add_rois(rois, types='scan')¶

Add the create_rois output and return the correct plots

Parameters

rois ((nd.array)) – the rois the user would like to add together
types ((str)) – either ‘scan’ or ‘bounding’ - depends on what roi’s the User sets for the rois variable

Returns

Return type

1d.array of the roi’s summed

sxdm.roi.bounding_box_setup(figure_class)¶

Set up the viewer figure for what bounding boxes have been selected

Parameters: (ROI_FigureClass) (figure_class) – the roi_figureclass object
Returns
Return type: Nothing - sets figure_class.axes

sxdm.roi.bounding_box_total_setup(user_class)¶

Complete setup of the summed diffraction pattern with the bounding boxes on top of them

Parameters: user_class ((SXDMFrameset)) – the sxdmframeset object
Returns
Return type: Nothing - sets up all the bounding box figures and loads all items

sxdm.roi.bounding_roi_figure_setup(figure_class)¶

Initiates the bounding box figure with axes

Parameters: (ROI_FiguresClass) (figure_class) – the roi_figuresclass object
Returns
Return type: Nothing

sxdm.roi.bounding_slider_setup(figure_class, user_class)¶

Sets up the bounding figure slider inside the roi figures

Parameters

(ROI_FiguresClass) (figure_class) – the roi_figuresclass object
(SXDMFrameset) (user_class) – the sxdmframeset object

Returns

Return type

Nothing

sxdm.roi.bounding_tb_setup(figure_class)¶

Sets up all the textboxes and buttons

Parameters: (ROI_FigureClass) (figure_class) – the roi_figureclass object
Returns
Return type: Nothing

sxdm.roi.close_all(event)¶

sxdm.roi.create_bounding_box_rois(fs)¶

sxdm.roi.create_total_linescan(fs)¶

sxdm.roi.display_left_roi(figure_class, user_class, types='scan')¶

Sets up the display for the left roi plot

Parameters

figure_class ((ROI_FigureClass)) – the roi_figureclass object
user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’

Returns

Return type

Nothing - displays the left roi figure

sxdm.roi.display_left_roi_reload(val, figure_class, user_class, types='scan')¶

Reloads the left roi

Parameters

val ((matplotlib event)) – the val matplotlib event
figure_class ((ROI_FigureClass)) – the roi_figureclass object
user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’

Returns

Return type

Nothing - reloads the left image

sxdm.roi.display_right_roi(figure_class, im)¶

Displays the right roi plot

Parameters

figure_class ((ROI_FigureClass)) – the roi_figureclass object
im ((nd.array)) – the image array to be displayed

Returns

Return type

Nothing - displays the right roi image

sxdm.roi.display_right_roi_reload(val, figure_class, im)¶

Load the Right ROI data

Parameters

val ((matplotlib event)) – the val matplotlib event
figure_class ((ROI_FigureClass)) – the roi_figureclass object
im ((nd.array)) – the image to be displayed

Returns

Return type

Nothing - reloads the right figure data

sxdm.roi.display_summed_ims(figure_class, user_class)¶

Show the summed diffraction pattern with all assigned bounding boxes

Parameters

figure_class ((ROI_FigureClass)) – the roi_figureclass object
user_class ((SXDMFrameset)) – the sxdmframeset object

Returns

Return type

Nothing - displays the summed diffraction pattern along with the User selected bounding boxes

sxdm.roi.display_summed_ims_reload(val, figure_class, user_class)¶

Allows the summed diffraction images to be displayed

Parameters

val ((matplotlib val)) – matplotlib variable
figure_class ((ROI_FigureClass)) – the roifigureclass object
user_class ((SXDMFrameset)) – the sxdmframeset object

Returns

Return type

Nothing - reloads the summed diffraction images in the figure

sxdm.roi.grab_int_v_scan(user_class, types='scan')¶

Grab the data needed for the gaus plot

Parameters

user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’ - determines which plots the User would like to get information for

Returns

Return type

Nothing - sets up the x and y values for the top plot of either the Scan ROI or the Bounding Box ROI

sxdm.roi.initiate_roi_viewer(user_class)¶

Sets up all the ROI viewer figures

Parameters: (SXDMFrameset) (user_class) – the sxdmframeset object
Returns
Return type: Nothing

sxdm.roi.on_scan_click(event, figure_class, user_class, types='scan')¶

Obtains all the raw scan data for a user clicked pixel

Parameters

(matplotlib event) (event) – the matplotlib event
(ROI_FiguresClass) (figure_class) – the roi_figuresclass object
(SXDMFrameset) (user_class) – the sxdmframeset object
(str) (types) – either ‘scan’ or ‘bounding’

Returns

Return type

Nothing - obtains all data and diplays data to appropriate location

sxdm.roi.right_roi(user_class, types='scan')¶

Plots the right roi plot

Parameters

user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’ - depends on which figure is being called

Returns

Return type

The entire summed region of interest for either the scans or the bounding boxes

sxdm.roi.scan_roi_figure_setup(figure_class)¶

Initiates the scan roi figure with proper axes locations current_roi_slider_val

Parameters: (ROI_FiguresClass) (figure_class) – the roi_figuresclass object
Returns
Return type: Nothing

sxdm.roi.scan_slider_setup(figure_class, user_class)¶

Sets up the scan figure slider inside the roi figures

Parameters

(ROI_FiguresClass) (figure_class) – the roi_figuresclass object
(SXDMFrameset) (user_class) – the sxdmframeset object

Returns

Return type

Nothing

sxdm.roi.start_bounding_roi(user_class)¶

Displays the bounding box roi with aproptiate textboxes

Parameters: (SXDMFrameset) (user_class) – the sxdmframeset object
Returns
Return type: Nothing

sxdm.roi.start_scan_roi(user_class)¶

Displays the scan roi figure with appropriate settings

Parameters: (SXDMFrameset) (user_class) – the sxdmframeset object
Returns
Return type: Nothing

sxdm.roi.textbox_setup(figure_class)¶

Sets up textboxes for the scan roi and the bounding box roi figures

Parameters: (ROI_FiguresClass) (figure_class) – the roi_figuresclass object
Returns
Return type: Nothing

sxdm.roi.top_plot_reload(val, figure_class, user_class, types='scan')¶

Reloads the gaus plot

Parameters

val ((matplotlib val)) – the value for matplot lib events
figure_class ((ROIFigure_Class)) – the roifigure_class objects
user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’ - determines which plots need to be reloaded

Returns

Return type

Nothing - reloads the top plot in the roi figures

sxdm.roi.top_plot_start(figure_class, user_class, types='scan')¶

Initiate the gaus plot

Parameters

figure_class ((ROI_FigureClass)) – the roi_figureclass object
user_class ((SXDMFrameset)) – the sxdmframeset object
types ((str)) – either ‘scan’ or ‘bounding’ allow the User to choose which figure they are working on

Returns

Return type

Nothing

sxdm.roi_bounding module¶

class sxdm.roi_bounding.ROI_FiguresClass¶

Bases: object

A class function which will make it easier to move variable in and out of functions

sxdm.roi_bounding.bounding_figure_setup(figure_class)¶

Set up the viewer figure

Parameters: (ROI_FigureClass) (figure_class) – the roi_figureclass object
Returns
Return type: Nothing - sets figure_class.axes

sxdm.roi_bounding.contbtn_click(event, figure_class, user_class)¶

Close the bounding box figure once complete

Parameters

(matplotlib event) (event) – the matplotlib event
(matplotlib figure) (fig) – the matplotlib figure to close

Returns

Return type

Nothing

sxdm.roi_bounding.line_select_callback(eclick, erelease, figure_class)¶

Creates interactive bounding boxes for roi analysis

Parameters

(event) (erelease) – the click event
(event) – the release event
(ROI_FigureClass) (figure_class) – the roi_figureclass object

Returns

Return type

Nothing

sxdm.roi_bounding.rec_select_setup(figure_class)¶

Initiate the rectangle interactive

Parameters: (ROI_FigureClass) (figure_class) – the roi_figureclass object
Returns
Return type: Nothing

sxdm.roi_bounding.rm_box_click(event, figure_class)¶

Removed the last bounding box the user made

Parameters

(matplotlib event) (event) – the matploblib event
(ROI_FigureClass) (figure_class) – the roi_figureclass object

Returns

Return type

Nothing

sxdm.roi_bounding.start_bounding_box(summed_diff_pattern, user_class)¶

Starts the ROI bounding box GUI

Returns
Return type: Nothing

sxdm.roi_bounding.textbox_btn_dropdown_setup(figure_class)¶

Sets up all the textboxes and buttons

Parameters: (ROI_FigureClass) (figure_class) – the roi_figureclass object
Returns
Return type: Nothing

sxdm.roi_bounding.vs_change(text, figure_class)¶

Change the vmin and vmax of a plot

Parameters

(matplotlib textbox) (text) – the matplotlib textbox
(ROI_FigureClass) (figure_class) – the roi_figureclass object

Returns

Return type

Nothing

sxdm.summed2d module¶

sxdm.summed2d.summed2d_all_data(self, bkg_multiplier=0)¶

Loads the summed diffraction patter without using a large amount of RAM

Parameters

(SXDMFrameset) (self) – the sxdmframeset object
(int) (bkg_multiplier) – the multiplier for the background images

Returns

Return type

the 2D summed diffraction pattern

sxdm.summed2d.summed2d_all_data_v2(self, bkg_multiplier=0)¶

Loads the summed diffraction patter without using a large amount of RAM

Parameters

(SXDMFrameset) (self) – the sxdmframeset object
(int) (bkg_multiplier) – the multiplier for the background images

Returns

Return type

the 2D summed diffraction pattern

sxdm.SXDM module¶

class sxdm.SXDM.SXDMFrameset(file, dataset_name, scan_numbers=False, fill_num=4, restart_zoneplate=False, median_blur_algorithm='scipy')¶

Bases: object

alignment(reset=False)¶

Allows the user to align all scans based on Fluorescence Maps or ROI Maps

Parameters: (bool) (reset) – if True this will clear all the alignment data. Use this when adding new scans to a group
Returns
Return type: Nothing - sets alignment data

centroid_analysis(rows, columns, med_blur_distance=9, med_blur_height=10, stdev_min=25, bkg_multiplier=1, slow=False, change_center=False, cores=0)¶

Calculates spot diffraction and data needed to make 2theta/chi/roi maps

Parameters

rows ((int, tup)) – the total number of rows you want to iterate through or a tuple of the rows to iterate through
columns ((int, tup)) – the total number of columns you want to iterate through or a tuple of the columns to iterate through
med_blur_distance ((int)) – the amount of values to scan for median blur
med_blur_height ((int)) – the height cut off for the median blur
stdev_min ((int)) – standard deviation above the mean of signal to ignore
bkg_multiplier ((int)) – multiplier for the background signal to be subtracted

Returns

Return type

the analysis results in the form of self.results

centroid_viewer(default_extents=False)¶

Allow the user to view the data in a convenient format

Parameters: (bool) (diffraction_load) – if True this will load all necessary data for the diffraction will take up at least 2gb of RAM
Returns
Return type: Nothing - displays viewer

chi_determination()¶: Determine the axis bounds for the diffraction images

frame_shape()¶

Returns the total imported scans shape (scan_number, rows, columns)

Parameters: (SXDMFrameset) (self) –
Returns
Return type: the frame set scan dimensions

gaus_checker(center_around=False, default=False)¶

Plots total diffraction intensity vs scan angle for a set ROI

Parameters

(bool) (default) – if True this will default the centerind index to the first index (0)
(bool) – if True this will default the roi to check the gaus of to the first user defined ROI

Returns

Return type

Nothing - displays the total intensity vs scan theta rocking curve

image_data_dimensions()¶

Determine the CCD image dimensions

Parameters: - SXDMFrameset (self) – the sxdmframeset
Returns
Return type: the image dimensions of the CCD camera

ims_array(amount2ave=3, multiplier=1, center_around=False)¶

Creates the Scan Background and the Image Array

Parameters

- int (amount2ave) – Take the first (amount2ave) to the last (amount2ave) pixels and use them as a background
- float (multiplier) – A number to be applied to the background image

Returns

Return type

Creates the background image and the image array used for many proceses

region_of_interest(rows, columns, med_blur_distance=9, med_blur_height=100, bkg_multiplier=1, diff_segmentation=True, slow=False, cores=0)¶

Create a region of interest map for each scan and center the region of interest maps. If the diff segmentation is True this will also create a region of interest map based on a user defined sub region of interests

Parameters

(int) or (tup) (columns) – the total amount of rows the user wants to do analysis on
(int) or (tup) – the total amount of columns the user wants to do analysis on
(int) (bkg_multiplier) – the amount of values to scan for median blur
(int) – the height cut off for the median blur
(int) – multiplier for the background signal to be subtracted
(bool) (diff_segmentation) – if set to True this will determine region of interests maps for sub roi’s set by the user

Returns

[(row, column), idxs,: raw_scan_data, corr_scan_data, scan_data_roi_vals, summed_data, corr_summed_data, summed_data_roi_vals]

Return type

the roi results in self.roi_results

reload_save(summed_dif_return=True)¶

Allow the user to reload Centroid saved data

Parameters: (bool) (summed_dif_return) – if True this will load all necessary data for the diffraction will take up at least 2gb of RAM
Returns
Return type: Nothing

roi_segmentation(bkg_multiplier=1, restart=False)¶

Allows the User to create a summed diffraction pattern bounding box for region_of_interest analysis

Parameters

(int) (bkg_multiplier) – the scaler applied to the background images
(bool) (restart) – if True this clears all bounding boxes when loading the segmentation data

Returns

Return type

Nothing

roi_viewer()¶

Takes the self.roi_results variable and displays it in a GUI format

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: Nothing

save()¶

Save self.results (Centroid Data) to _savedata.h5

Unable to efficiently save ROI data

sxdm.viewer module¶

class sxdm.viewer.FiguresClass¶

Bases: object

A class function which will make it easier to move variable in and out of functions

sxdm.viewer.analysis_change(text, self)¶

When analysis values change, make the plots change as well to fit analysis parameters :param text (textbox text event): textbox text event :param self (SXDMFrameset): the sxdmframeset

Returns
Return type: Nothing - loads figure data

sxdm.viewer.btn_setup(reproocessbtn_ax, savingbtn_ax)¶

Set up the reprocess and saving button

Parameters

reproocessbtn_ax ((matplotlib axis)) – the reproocess button figure axis
savingbtn_ax ((matplotlib axis)) – the saving button figure axis

Returns

Return type

reprocess and saving button

sxdm.viewer.convert_x_axis(intensity_values, extents, centroid_value, type='ttheta')¶

sxdm.viewer.figure_setup()¶

Set up the viewer figure

Returns
Return type: All axes for the figure

sxdm.viewer.image_array_bkg_check(self)¶

Warns the User if they have not started the create_imagearray() or scan_background() functions

Parameters: self –
Returns

sxdm.viewer.load_dynamic_data(results, vmin_spot, vmax_spot, spot_dif_ax, ttheta_centroid_ax, chi_centroid_ax, med_blur_distance, med_blur_height, stdev_min, row, column, self)¶

Load the dynamic data in the viewer based on the user inputs :param results (nd.array): the output of self.analysis or the self.results value :param vmin_spot (int): the vmin for the summed diffraction spot image :param vmax_spot (int): the vmax for the summed diffraction spot image :param spot_dif_ax (matplotlib axis): the figure axis for the diffraction spot image :param ttheta_centroid_ax (matplotlib axis): the figure axis for the 1D two theta plot :param chi_centroid_ax (matplotlib axis): the figure axis for the 1D chi plot :param med_blur_distance (int): the integer value used in the median_blur() function :param med_blur_height (int): the integer value used in the median_blur() function :param stdev_min (int): the standard deviation value used in the median_blur() segmentation function :param row (int): the row the user would like to load the data for :param column (int): the bolumn the user would like to load the data for :param self (SXDMFramset): the sxdmframset

Returns
Return type: Nothing - loads figure data

sxdm.viewer.load_static_data(results, vmin_sum, vmax_sum, fluor_ax, roi_ax, summed_dif_ax, ttheta_map_ax, chi_map_ax, fluor_image, user_class=False)¶

Load all the static data for the viewer :param results (nd.array): the output of the self.analysis function or the self.results value :param vmin_sum (int): the vmin for the summed diffraction image :param vmax_sum (int): the vmax for the summed diffraction image :param fluor_ax (matplotlib axis): the figure axis for the fluorescence image :param roi_ax (matplotlib axis): the figure axis for the region of interest image :param summed_dif_ax (matplotlib axis): the figure axis for the summed diffraction image :param ttheta_map_ax (matplotlib axis): the figure axis for the 2theta centroid map :param chi_map_ax (matplotlib axis): the figure axis for the chi centroid map :param fluor_image (image array): the fluorescence image the user would like to display in the figure :param user_class (SXDMFrameset): the sxdmframeset object or False

Returns
Return type: Nothing - displays figure images

sxdm.viewer.make_black(self)¶

Reset figures to black when everything is up to date :param self (SXDMFrameset): the sxdmframeset

Returns
Return type: Nothing - loads figure formatting

sxdm.viewer.make_pink(self)¶

Show the user which values have not been saved by turning them pink :param self (SXDMFrameset): the sxdmframeset

Returns
Return type: Nothing - loads figure formatting

sxdm.viewer.make_red(self)¶

Show the user which figures are not current by turning them red :param self (SXDMFrameset): the sxdmframeset

Returns
Return type: Nothing - loads figure formatting

sxdm.viewer.reload_some_static_data(results, roi_ax, ttheta_map_ax, chi_map_ax)¶

Reloading some of the static data when you save/reload image :param results (nd.array): the output of the self.analysis function or the self.results value :param roi_ax (matplotlib axis): the figure axis for the region of interest map :param ttheta_map_ax (matplotlib axis): the figure axis for the 2theta centroid map :param chi_map_ax (matplotlib axis): the figure axis for the chi centroid map

Returns
Return type: Nothing - displays figure images

sxdm.viewer.reprocessbtn_click(event, user_class, figure_class)¶

Calls the self.analysis function once the reprocessed button is clicked :param event (matplotlib event): matplotlib event :param user_class (SXDMFrameset): the sxdmframeset :param figure_class (FigureClass): the figureclass

Returns
Return type: Nothing - loads figure formatting

sxdm.viewer.run_viewer(user_class, fluor_image)¶

Function that compiles functions to get the viewer working :param user_class (SXDMFrameset): the sxdmframeset :param fluor_image (image): the fluorescence image the user would like to load into the viewer

Returns
Return type: Nothing - loads figure data

sxdm.viewer.savingbtn_click(event, user_class, figure_class)¶

Calls the self.save function and reloads data to the viewer :param event (matplotlib event): matplotlib event :param user_class (SXDMFrameset): the sxdmframeset :param figure_class (FigureClass): the figureclass

Returns
Return type: Nothing - loads figure formatting

sxdm.viewer.spot_change(text, self)¶

When the user changes texbox value spots on the image, reload all the data for the new spot :param text (texbox text event): textbox text event :param self (CurrentFigure Class): the currecnt figure class

Returns
Return type: Nothing - loads figure data

sxdm.viewer.spot_dif_ram_save(self)¶

Allows the program to take all the user_class.image_array images and sum them together to get a single summed diffraction image

Parameters: (SXDMFrameset) (self) – the sxdmframeset object
Returns
Return type: the summed diffraction image for the entire FOV set by the create_imagearray() function

sxdm.viewer.sum_error()¶

If there is an error loading data, import psyduck

Returns
Return type: psyduck image

sxdm.viewer.tb_setup(vmin_spot_ax, vmax_spot_ax, vmin_sum_ax, vmax_sum_ax, med_blur_dis_ax, med_blur_h_ax, stdev_ax, multiplier_ax, self)¶

Set up all textboxes :param vmin_spot_ax (matplotlib axis): the figure axis that goes to the vmin change for the spot diffraction :param vmax_spot_ax (matplotlib axis): the figure axis that goes to the vmax change for the spot diffraction :param vmin_sum_ax (matplotlib axis): the figure axis that goes to the vmin change for the summed diffraction :param vmax_spot_ax (matplotlib axis): the figure axis that goes to the vmax change for the summed diffraction :param med_blur_dis_ax (matplotlib axis): the figure axis that goes to the median blur distance value :param med_blur_h_ax (matplotlib axis): the figure axis that goes to the median blur height value :param stdev_ax (matplotlib axis): the figure axis that goes to the standard deviation value :param multiplier_ax (matplotlib axis): the figure axis that goes to the background multiplier value :param self (SXDMFrameset): the sxdmframset

Returns
Return type: All textboxes associated with these axis

sxdm.viewer.viewer_mouse_click(event, self)¶

Based on what is clicked in the figure change the viewer accordingly :param event (matplotlib event): matplotlib event :param self (FigureClass): the figureclass object

Returns
Return type: Nothing - loads figure formatting