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

data¶: Alias for field number 5

data_id¶: Alias for field number 4

fabio_image¶: Alias for field number 3

frame_id¶: Alias for field number 2

header¶: Alias for field number 6

source¶: Alias for field number 0

source_filename¶: Alias for field number 7

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()¶

pyFAI.app package¶

pyFAI.app.average module¶

pyFAI.app.benchmark module¶

pyFAI.app.calib module¶

pyFAI.app.calib2 module¶

pyFAI.app.check_calib module¶

pyFAI.app.detector2nexus module¶

pyFAI.app.diff_map module¶

pyFAI.app.diff_tomo module¶

pyFAI.app.drawmask module¶

pyFAI.app.eiger_mask module¶

pyFAI.app.integrate module¶

pyFAI.app.mx_calibrate module¶

pyFAI.app.recalib module¶

pyFAI.app.saxs module¶

pyFAI.app.setup module¶

pyFAI.app.waxs module¶

Module contents¶

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