pyFAI.app package¶
pyFAI.app.average module¶
utility that averages out a serie of files
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class
pyFAI.app.average.
ShellAverageObserver
¶ Bases:
pyFAI.average.AverageObserver
Display average processing using a shell progress bar
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__init__
()¶
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algorithm_finished
(algorithm)¶
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algorithm_started
(algorithm)¶
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frame_processed
(algorithm, frame_index, frames_count)¶
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hide_info
()¶
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image_loaded
(fabio_image, image_index, images_count)¶
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process_finished
()¶
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process_started
()¶
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result_processing
(algorithm)¶
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show_info
()¶
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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.
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pyFAI.app.average.
main
()¶
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pyFAI.app.average.
parse_algorithms
(options)¶ Return a list of initilized algorithms from the command line
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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
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pyFAI.app.benchmark.
main
()¶
pyFAI.app.calib module¶
CLI tool for determining the geometry of a detector using a reference sample.
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pyFAI.app.calib.
main
()¶
pyFAI.app.calib2 module¶
GUI tool for determining the geometry of a detector using a reference sample.
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pyFAI.app.calib2.
configure_parser_arguments
(parser)¶
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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.
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pyFAI.app.calib2.
logUncaughtExceptions
(exceptionClass, exception, stack)¶
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pyFAI.app.calib2.
main
()¶
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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
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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
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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
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pyFAI.app.check_calib.
main
()¶
pyFAI.app.detector2nexus module¶
Converts a detector description into a NeXus detector usable by other pyFAI utilities
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pyFAI.app.detector2nexus.
main
()¶
pyFAI.app.diff_map module¶
GUI interface for reduction of diffraction tomography experiments
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pyFAI.app.diff_map.
main
()¶
pyFAI.app.diff_tomo module¶
CLI interface for diffraction tomography data reduction
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class
pyFAI.app.diff_tomo.
DiffTomo
(nTrans=1, nRot=1, nDiff=1000)¶ Bases:
pyFAI.diffmap.DiffMap
Basic class for diffraction tomography experiment using pyFAI.
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__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
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parse
(with_config=False)¶ parse options from command line
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pyFAI.app.diff_tomo.
main
()¶
pyFAI.app.drawmask module¶
Use silx library to provide a widget to customize a mask
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class
pyFAI.app.drawmask.
AbstractMaskImageWidget
¶ Bases:
PyQt5.QtWidgets.QMainWindow
Abstract window application which allow to create a mask manually.
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__init__
()¶
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saveAndClose
()¶
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setOutputFile
(outputFile)¶
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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.
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__init__
()¶
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getSelectionMask
()¶
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setImageData
(image)¶
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pyFAI.app.drawmask.
main
()¶
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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.
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pyFAI.app.eiger_mask.
extract_mask
(infile)¶ Retrieve the mask from an Eiger master file.
Parameters: infile – name of the Eiger master file
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pyFAI.app.eiger_mask.
main
()¶
pyFAI.app.integrate module¶
GUI tool for configuring azimuthal integration on series of files.
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class
pyFAI.app.integrate.
DataInfo
(source, source_id, frame_id, fabio_image, data_id, data, header, source_filename)¶ Bases:
tuple
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data
¶ Alias for field number 5
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data_id
¶ Alias for field number 4
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fabio_image
¶ Alias for field number 3
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frame_id
¶ Alias for field number 2
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header
¶ Alias for field number 6
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source
¶ Alias for field number 0
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source_filename
¶ Alias for field number 7
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source_id
¶ Alias for field number 1
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class
pyFAI.app.integrate.
DataSource
(statistics)¶ Bases:
object
Source of data to integrate.
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__init__
(statistics)¶
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append
(item)¶
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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
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basename
()¶ Returns a basename identifying this data source
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count
()¶
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frames
()¶ Iterate all the frames from this data source.
Return type: Iterator[DataInfo]
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is_multiframe
()¶
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is_single_multiframe
()¶
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class
pyFAI.app.integrate.
IntegrationObserver
¶ Bases:
object
Interface providing access to the to the processing of the process function.
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__init__
()¶
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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.
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is_interruption_requested
()¶
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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
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processing_finished
()¶ Called when the full processing is finisehd (interupted or not).
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processing_interrupted
(reason=None)¶ Called before processing_finished if the processing was interrupted.
Parameters: error ([str,Exception,None]) – A reason of the interruption.
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processing_started
(data_count)¶ Called before starting the full processing.
Parameters: data_count (int) – Number of data to integrate
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processing_succeeded
()¶ Called before processing_finished if the processing succedded.
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request_interruption
()¶
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worker_initialized
(worker)¶ Called when the worker is initialized
Parameters: data_count (int) – Number of data to integrate
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class
pyFAI.app.integrate.
MultiFileWriter
(output_path, mode='error')¶ Bases:
pyFAI.io.Writer
Broadcast writing to differnet files for each frames
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__init__
(output_path, mode='error')¶
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close
()¶
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init
(fai_cfg=None, lima_cfg=None)¶
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prepare_write
(data_info, engine)¶
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write
(data)¶
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class
pyFAI.app.integrate.
ShellIntegrationObserver
¶ Bases:
pyFAI.app.integrate.IntegrationObserver
Implement IntegrationObserver as a shell display.
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__init__
()¶
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hide_info
()¶
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processing_data
(data_info, approximate_count=None)¶
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processing_finished
()¶
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processing_started
(data_count)¶
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show_info
()¶
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class
pyFAI.app.integrate.
Statistics
¶ Bases:
object
Instrument the application to collect statistics.
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__init__
()¶
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execution_finished
()¶
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execution_started
()¶
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preprocessing
()¶ Try to extract the preprocessing time
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processing_per_frame
()¶ Average time spend to process a frame
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reading_per_frame
()¶ Average time spend to read a frame
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time_processing
()¶
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time_reading
()¶
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total_execution
()¶
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total_processing
()¶
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total_reading
()¶
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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
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pyFAI.app.integrate.
integrate_gui
(options, args)¶
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pyFAI.app.integrate.
integrate_shell
(options, args)¶
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pyFAI.app.integrate.
main
()¶
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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
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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.
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pyFAI.app.recalib.
main
()¶
pyFAI.app.saxs module¶
Integrate 2D images into SAXS patterns. Also used in PDF measurements
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pyFAI.app.saxs.
main
()¶
Module contents¶
Common for all applications within pyFAI