pyFAI.app package

pyFAI.app.average module

utility that averages out a serie of files

class pyFAI.app.average.ShellAverageObserver

Bases: pyFAI.average.AverageObserver

Display average processing using a shell progress bar

__init__()

Initialize self. See help(type(self)) for accurate signature.

algorithm_finished(algorithm)

Called when an algorithm is finished

algorithm_started(algorithm)

Called when an algorithm is started

frame_processed(algorithm, frame_index, frames_count)

Called after providing a frame to an algorithm

hide_info()

image_loaded(fabio_image, image_index, images_count)

Called when an input image is loaded

process_finished()

Called when the full process is finished

process_started()

Called when the full processing is started

result_processing(algorithm)

Called before the result of an algorithm is computed

show_info()

pyFAI.app.average.cleanup_input_paths(input_paths)

Clean up filename using :: to access to data inside file.

Returns

Returns a list of paths without directory separator inside the filename location.

pyFAI.app.average.main()

pyFAI.app.average.parse_algorithms(options)

Return a list of initilized algorithms from the command line

pyFAI.app.average.parse_writer(input_images, options, algorithms)

Return a writer by using information from the command line

pyFAI.app.benchmark module

utility to run the benchmark for azimuthal integration on images of various sizes

pyFAI.app.benchmark.main()

pyFAI.app.calib module

CLI tool for determining the geometry of a detector using a reference sample.

pyFAI.app.calib.main()

pyFAI.app.calib2 module

GUI tool for determining the geometry of a detector using a reference sample.

pyFAI.app.calib2.configure_parser_arguments(parser)

pyFAI.app.calib2.displayExceptionBox(message, exc_info)

Display an exception as a MessageBox

Parameters

• message (str) – A context message

• exc_info (Union[tuple,Exception]) – An exception or the output of exc_info.

pyFAI.app.calib2.logUncaughtExceptions(exceptionClass, exception, stack)

pyFAI.app.calib2.main()

pyFAI.app.calib2.parse_options()

Returns parsed command line argument as an options object.

Raises

ExitException – In case of the use of –help in the comman line

pyFAI.app.calib2.parse_pixel_size(pixel_size)

Convert a comma separated sting into pixel size

Parameters

pixel_size (str) – String containing pixel size in micron

Return type

Tuple[float,float]

Returns

Returns floating point pixel size in meter

pyFAI.app.calib2.setup_model(model, options)

Setup the model using options from the command line.

Parameters

model (pyFAI.gui.model.CalibrationModel) – Model of the application

pyFAI.app.check_calib module

DEPRECATED tool that checks a calibratation at the sub-pixel level

pyFAI.app.check_calib.main()

pyFAI.app.detector2nexus module

Converts a detector description into a NeXus detector usable by other pyFAI utilities

pyFAI.app.detector2nexus.main()

pyFAI.app.diff_map module

GUI interface for reduction of diffraction tomography experiments

pyFAI.app.diff_map.main()

pyFAI.app.diff_tomo module

CLI interface for diffraction tomography data reduction

class pyFAI.app.diff_tomo.DiffTomo(nTrans=1, nRot=1, nDiff=1000)

Bases: pyFAI.diffmap.DiffMap

Basic class for diffraction tomography experiment using pyFAI.

__init__(nTrans=1, nRot=1, nDiff=1000)

Constructor of the class

Parameters

• nTrans – number of translations

• nRot – number of translations

• nDiff – number of points in diffraction pattern

parse(with_config=False)

parse options from command line

pyFAI.app.diff_tomo.main()

pyFAI.app.drawmask module

Use silx library to provide a widget to customize a mask

class pyFAI.app.drawmask.AbstractMaskImageWidget

Bases: PyQt5.QtWidgets.QMainWindow

Abstract window application which allow to create a mask manually.

__init__()

Initialize self. See help(type(self)) for accurate signature.

saveAndClose()

setOutputFile(outputFile)

class pyFAI.app.drawmask.MaskImageWidget

Bases: pyFAI.app.drawmask.AbstractMaskImageWidget

Window application which allow to create a mask manually. It is based on Silx library widgets.

__init__()

Initialize self. See help(type(self)) for accurate signature.

getSelectionMask()

setImageData(image)

pyFAI.app.drawmask.main()

pyFAI.app.drawmask.postProcessId21(processFile, mask)

Post process asked by Marine Cotte (ID21)

TODO: Remove it outside if it is possible. Ask them if it is still used.

pyFAI.app.eiger_mask module

extracts the mask from an Eiger master file.

pyFAI.app.eiger_mask.extract_mask(infile)

Retrieve the mask from an Eiger master file.

Parameters

infile – name of the Eiger master file

pyFAI.app.eiger_mask.main()

pyFAI.app.integrate module

GUI tool for configuring azimuthal integration on series of files.

class pyFAI.app.integrate.DataInfo(source, source_id, frame_id, fabio_image, data_id, data, header, source_filename)

Bases: tuple

property data

Alias for field number 5

property data_id

Alias for field number 4

property fabio_image

Alias for field number 3

property frame_id

Alias for field number 2

property header

Alias for field number 6

property source

Alias for field number 0

property source_filename

Alias for field number 7

property source_id

Alias for field number 1

class pyFAI.app.integrate.DataSource(statistics)

Bases: object

Source of data to integrate.

__init__(statistics)

Initialize self. See help(type(self)) for accurate signature.

append(item)

approximate_count()

Returns the number of frames contained in the data source.

To speed up the processing time, this value could be approximate. Especially with file series, and EDF multiframes.

Type

int

basename()

Returns a basename identifying this data source

count()

frames()

Iterate all the frames from this data source.

Return type

Iterator[DataInfo]

is_multiframe()

is_single_multiframe()

class pyFAI.app.integrate.IntegrationObserver

Bases: object

Interface providing access to the to the processing of the process function.

__init__()

Initialize self. See help(type(self)) for accurate signature.

data_result(data_info, result)

Called after each data processing, with the result

Parameters

• data_info (DataInfo) – Contains data and metadata from the data to integrate

• result (object) – Result of the integration.

is_interruption_requested()

processing_data(data_info, approximate_count=None)

Start processing the data data_info

Parameters

• data_info (DataInfo) – Contains data and metadata from the data to integrate

• approximate_count (int) – If set, the amount of total data to process have changed

processing_finished()

Called when the full processing is finisehd (interupted or not).

processing_interrupted(reason=None)

Called before processing_finished if the processing was interrupted.

Parameters

error ([str,Exception,None]) – A reason of the interruption.

processing_started(data_count)

Called before starting the full processing.

Parameters

data_count (int) – Number of data to integrate

processing_succeeded()

Called before processing_finished if the processing succedded.

request_interruption()

worker_initialized(worker)

Called when the worker is initialized

Parameters

data_count (int) – Number of data to integrate

class pyFAI.app.integrate.MultiFileWriter(output_path, mode='error')

Bases: pyFAI.io.Writer

Broadcast writing to differnet files for each frames

__init__(output_path, mode='error')

Constructor of the class

close()

init(fai_cfg=None, lima_cfg=None)

Creates the directory that will host the output file(s) :param fai_cfg: configuration for worker :param lima_cfg: configuration for acquisition

prepare_write(data_info, engine)

write(data)

To be implemented

class pyFAI.app.integrate.ShellIntegrationObserver

Bases: pyFAI.app.integrate.IntegrationObserver

Implement IntegrationObserver as a shell display.

__init__()

Initialize self. See help(type(self)) for accurate signature.

hide_info()

processing_data(data_info, approximate_count=None)

Start processing the data data_info

Parameters

• data_info (DataInfo) – Contains data and metadata from the data to integrate

• approximate_count (int) – If set, the amount of total data to process have changed

processing_finished()

Called when the full processing is finisehd (interupted or not).

processing_started(data_count)

Called before starting the full processing.

Parameters

data_count (int) – Number of data to integrate

show_info()

class pyFAI.app.integrate.Statistics

Bases: object

Instrument the application to collect statistics.

__init__()

Initialize self. See help(type(self)) for accurate signature.

execution_finished()

execution_started()

preprocessing()

Try to extract the preprocessing time

processing_per_frame()

Average time spend to process a frame

reading_per_frame()

Average time spend to read a frame

time_processing()

time_reading()

total_execution()

total_processing()

total_reading()

pyFAI.app.integrate.get_monitor_value(image, monitor_key)

Return the monitor value from an image using an header key.

Parameters

• image (fabio.fabioimage.FabioImage) – Image containing the header

• monitor_key (str) – Key containing the monitor

Returns

returns the monitor else returns 1.0

Return type

float

pyFAI.app.integrate.integrate_gui(options, args)

pyFAI.app.integrate.integrate_shell(options, args)

pyFAI.app.integrate.main()

pyFAI.app.integrate.process(input_data, output, config, monitor_name, observer, write_mode='error')

Integrate a set of data.

Parameters

• input_data (List[str]) – List of input filenames

• output (str) – Filename of directory output

• config (dict) – Dictionary to configure pyFAI.worker.Worker

• observer (IntegrationObserver) – Observer of the processing

• write_mode (str) – Specify options to deal with IO errors

pyFAI.app.mx_calibrate module

calibrate the distance of a detector from a set of powder diffraction patterns

pyFAI.app.mx_calibrate.main()

pyFAI.app.recalib module

DEPRECATED tool for refining the geometry of a detector using a reference sample and a previously known calibration file.

pyFAI.app.recalib.main()

pyFAI.app.saxs module

Integrate 2D images into SAXS patterns. Also used in PDF measurements

pyFAI.app.saxs.main()

pyFAI.app.setup module

pyFAI.app.setup.configuration(parent_package='', top_path=None)

pyFAI.app.waxs module

Integrate 2D images into powder diffraction patterns

pyFAI.app.waxs.main()

Module contents

Common for all applications within pyFAI