Improve background task handling (#116)

* introduce “task manager” to improve synchronization of data loading and reconstruction tasks; implement blocking option for diffraction data loading and reconstruction tasks
* several breaking API changes: renamed scan -> probe positions based on user feedback, add option to disable diffraction pattern processing
* implement reconstruction progress monitoring
* fix bad pixels handling and add documentation for good/bad pixel masks
* simplify behavior of crop center editing widgets
* closing diffraction dataset clears visualization
* rework stxm analysis dialog to stxm object builder
* improve object fourier analysis dialog and promote from developer mode
* extract globus integration from workflow module
* rename ptychoshelves readers -> fold_slice readers; fix loss value loading
* change default hdf5 file writer compression method to lzf
* fix fresnel zone plate probe builder for rectangular probes
* display current object and probe pixel sizes in GUI
* remove tike integration
* add convert-to-ptychodus script for translating prepared datasets to ptychodus file format
* update ptychouds-bdp script and batch mode actions to use standard directory layout
* standardize argument naming across scripts
* add convert-to-ptychodus and ptychodus-bdp to project scripts

Author: stevehenke

README.rst

@@ -1,12 +1,11 @@
 Ptychodus
 =========
 
-`Ptychodus <https://github.com/AdvancedPhotonSource/ptychodus>`_
-is a ptychography data analysis application that reads instrument data,
-prepares the data for processing, and supports calling several reconstruction
-libraries for phase retrieval. Ptychodus can be used interactively or
-integrated into a data pipeline.
-
+`Ptychodus <https://github.com/AdvancedPhotonSource/ptychodus>`_ is a
+ptychography data analysis application that extracts, loads, and transforms
+instrument data for processing. It integrates several reconstruction libraries
+for phase retrieval. Ptychodus can be used interactively or integrated into
+beamline data pipelines.
 
 Standard Installation
 ---------------------

docs/source/readers.rst

@@ -35,3 +35,16 @@ be happy to add file readers to support more ptychography instruments.
     - Ptychodus Product (*.h5, *.npz)
     - Space-Separated Values (*.txt)
     - Tagged Image File Format (*.tif, *.tiff)
+
+Good/Bad Pixel Masks
+====================
+
+Currently there are two numpy (NPY) file formats that can be used to indicate
+detector pixels that are usable ("good pixels") or unusable ("bad pixels") for
+processing. Both file types contain a 2-D boolean array with the same dimensions
+as an unprocessed detector frame. For the "good pixels" format, True indicates a
+usable pixel and False indicates an unusable pixel. For the "bad pixels" format,
+True indicates an unusable pixel and False indicates a usable pixel. When one of
+these files is provided, Ptychodus will zero bad pixels and provide the mask to
+processing algorithms that support pixel masks. When one of these files is not
+provided, Ptychodus assumes that all pixels should be used for processing.

globus.svg

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ptychodus"
-description = "Ptychodus is a ptychography data analysis application."
+description = "Ptychodus is a ptychography data pipeline application."
 readme = "README.rst"
 requires-python = ">=3.10"
 license = "BSD-3-Clause"
@@ -25,13 +25,14 @@ dependencies = [
 dynamic = ["version"]
 
 [project.scripts]
+convert-to-ptychodus = "ptychodus.convert_to_ptychodus:main"
 ptychodus = "ptychodus.__main__:main"
+ptychodus-bdp = "ptychodus.ptychodus_bdp:main"
 
 [project.optional-dependencies]
 globus = ["gladier", "gladier-tools>=0.5.4"]
 gui = ["PyQt5"]
 ptychonn = ["ptychonn==0.3.*,>=0.3.7"]
-tike = ["tike==0.25.*,>=0.25.3"]
 ptychi = ["ptychi==1.*,>=1.2.0"]
 
 [tool.setuptools.package-data]
@@ -59,7 +60,6 @@ module = [
     "pvapy.*",
     "scipy.*",
     "tifffile",
-    "tike.*",
 ]
 ignore_missing_imports = true