Changelog#
2.0: unreleased#
1.0.2#
Bug fixes:
handle processing from CLI for HDF5
fix dimension fitting
remember previous selected filename for HDF5 dataset
1.0.1#
Bug fixes:
Fix scikit-image dependency versions
Handle API changes of
skimage.registration.phase_correlation
Fix
load_process_data
for a string URLFix
darfix.core.dimension.Dimension.set_unique_values
when dimension values and step size are small
1.0.0#
New features:
Support HDF5 (including positioners)
Widget to recover weak beam to obtain dislocations
Add top-threshold to the noise removal widhet
Bug fixes:
Upper bound on silx and orange3 packages
ROISelectionWidget: reset ROI for new datasets
TransformationWidgetOW: reset dimensions for new datasets
Fix dtype bug in dataset NMF (blind source separation)
Support latest PyQt5 API changes
Changes:
Use named tuples when passing data between tasks
Provide meanigful message when no dataset provided
0.10.0#
Allow ROI selection with integer numbers (by manually typing them)
Fix data appearing outside of defined dimensions range
Reduce memory usage
0.9.8#
fix Mapping import bug
0.9.7#
reduce memory usage in the rebinning task
partition data widget: range of histogram X-axis based on the number of bins and not intensity
rename “in disk” to “on disk”
make all directory creation recursive
clear the mask in the noise removal widget when the ROI changes
fix rocking curve map names when exporting
ignore flash widget in batch processing
0.9.6#
opencv-python<4.7 for python 3.6
fix RSM histogram axes
0.9.5#
support numpy >= 1.24
0.9.4#
fix mask error in noiseRemovalWidget
0.9.3#
fix plot axes in grainPlotWidget, zSumWidget and rockingCurvesWidget when an axes transformation is involved
handle NaNs in datasets
0.9.2#
opencv-python==4.3.0.36 is not on pypi so make it opencv-python>=4.3.0.36
0.9.1#
proper project structure
fix orangecontrib namespace package
ewoks lower version bounds
0.9.0#
Core:
mapping.py
:Add binning function (MR !174)
Add RSM Histogram function based on Mads Carlsen scripts (MR !176)
Improve calculation of RSM to take into account angle tilt (use eta insatead of chi) (MR !176)
dataset.py
:Add
apply_binning
method (MR !174)Add
apply_mask_removal
method and MASK operation (MR !179)Add
compute_rsm
method (MR !176)Append “fake” values to metadata when data is HDF5 (MR !182)
Mosaicity: Add third motor parameter and option to choose dimensions to use(MR !177)
Project: Allow 2D projection (MR !177)
Metadata: Allow for empty rows by setting them to 0 (MR !180)
Find dimensions: Return False if dataset is H5 (no dimensions in this case) (MR !182)
dimensions.py
: Sort items of dictionary (MR !181) and return empty dict if no dims when converting to dictionary (MR !182)imageOperations.py
: Addmask_removal
function (MR !179)process.py
: Add mask parameter inNoiseRemoval
(MR !179) and addRSMHistogram
function (MR !176)
GUI:
Create widget for binning (MR !174)
Add RSMHistogramWidget (MR !176)
noiseRemovalWidget.py
: Add mask property (MR !179)utils.pt
: Addvalues
and_filter
attributes inChooseDimensionWidget
(MR !177)grainPlotWidget.py
:Add option to choose motors in ori dist and mosaicity maps for 3D datasets(MR !177)
Save origine attribute when exporting ori dist and remove minimum size for window (MR !181)
Show error message if there are no dimensions defined (MR !182)
projectionWidget.py
: UseChooseDimensionWidget
to choose dimensions to project (MR !177)dimensionsWidget.py
: Show error message when trying to find dimensions in H5 dataset (MR !182)
examples: Add binning example (MR !174) and rsmHistogram example (MR !176). Fix typo with keys in
plot_ori_dist
(MR !181)orangecontrib: Add binning widget and its icon (MR !174) and rsmHistogram widget (MR !176)
0.8.0#
Change needed opencv-python version to fix bug (4.3.0.36) (MR !155)
Core:
process.py
: Add optional_input_names missing as input parameters (MR !162) and add Projection class (MR !155)dataset.py
:Dataset:
Remove temporary directories (MR !166)
Fit: Remove loop along dimensions and return fitted parameters (MR !170)
Add title attribute (MR !154)
Add
project_data
method to return a new Dataset with the projected data (MR !155)Partition: Add option to filter by top bin (MR !173)
Projection: Only add projected image if exists and fix typo with metadata values (MR !169)
Shift: Use h5py copy function to avoid loading dataset on memory (MR !169)
Orientation distribution: Compute for more than 1 dimensions dataset using first two dimensions (MR !169)
PCA: Temporarily set a fixed number of chunks to avoid memory errors on big datasets (MR !169)
Data:
Save: Use indices to not copy all data if not needed (MR !175) and filter by indices after flattening (MR !171)
dimension.py
(MR 169):Add
unique_values
inDimension
__init__
Convert axis to
int
before converting dictionary toDimension
mapping.py
:Return fitted parameters with rocking curves (MR !170)
Add multi_gaussian method (MR !155)
Add 2D rocking curve fit and 2D data fit (MR !155)
Return FWHM value instead of std both in moments and rocking methods (MR !172)
Add indices in generator and use them for 2D fit (MR !169)
Make sure bounds are feasible when fiting rocking curves and set lower bound of std to 0 (MR !171)
utils.py
:Create function to create NXdata in dict form (MR !172)
test
:partition.py
: Computer partition using range (MR !173)dimension.py
: Add 2D fit test method (MR !169)
Decomposition (MR !169):
base.py
: Use indices when computing error
GUI:
Add optional title into plots (MR !154)
dataSelectionWidget.py
: Add option to enter workflow title (MR !154)magnificationWidget.py
: Add Orientation Enum class to define orientations (MR !160)shiftCorrectionWidget.py
: Fix error when filtering data after data partition (MR !167)rockingCurvesWidget.py
:Add
Background
map replaceIntegrated intensity
forAmplitude
(MR !170)Use fitted parameters to show the maps (MR !170)
Remove “filter by dimension” option (MR !170)
Change
Method
class toMaps
and addMaps_2D
class to enumerate the maps when having 2D data (MR !155)Show label with parameters for each rocking curve (MR !155)
Apply transformation if any (MR !155)
Show image with fitted contours instead of rocking curve with 2D datasets (MR !155)
Export 2D maps (MR !155) and use NXdata for each (MR !172)
Add residuals property (MR! 172)
Use plotRockingCurves method when changing stackview frame and put zeros in unused indices (MR !169)
grainPlotWidget.py
:Add option to center the axes or use motor values in orientation distribution (MR !155)
Create property for mosaicity (MR !172)
Export maps: create NXdata for each map, and add transformation axes if necessary
dataPartitionWidget.py
: Compute partition using range (MR !173)noiseRemovalWidget.py
: Add DATA_TYPES Enum (MR !173)utils.py
: Addvertical
parameter inChooseDimensionWidget
to set orientation of widget (MR !169)displayComponentsWidget.py
:Use
ChooseDimensionWidget
to filter by dimension and add corresponding methods to filter and unfilter (MR !169)Use
indices
when applying threshold (MR !175)
linkComponentsWidget.py
: Convert dimensions toAcquisitionDims
(MR !169)Create new widget “ProjectionWidget” to reduce the number of data in a 2D dataset by projecting one of the dimensions (MR !155)
IO:
utils.py
: Modify read and write compontents functions to save/read to/from dimensions dictionary and to save dimensions values(MR !169)examples: Add projection example (MR !155)
orangecontrib: Add
projection.py
widget (MR !155)gitlab-ci: Add continous deployment and tests for win32 (MR !163)
0.7.3#
Core:
mapping.py
: Convert list to numpy array to allow calculate ptp() (MR !152)dataset.py
:Dataset:
Append url to urls list to avoid error when not fitting (MR !152)
bs/hp/tr: Create temporary hdf5 file to save the new data in case of data partition(MR !159)
Data: Modify save() method to reshape modified urls to previous shape (MR !159)
test
:Dataset: Add tests that use hdf5 as input (MR !159)
GUI:
rockingCurvesWidget.py
: Add export maps option (MR !152)roiSelectionWidget.py
: Fix bug when ROI is None (MR !157)dimensionsWidget.py
: Fix typo when computing unique values with more than two dimensions (MR !158)displayComponentsWidget.py
: Create MixingPlotsWidget (MR !158)linkComponentsWidget.py
: Only show scatter if number of dimensions is 2 (MR !158)
io:
utils.py
: Write components with shape parameter (MR !158)
0.7.2#
Core (!MR 156):
dataset.py
: Remove unusedtreated
property.data_selection.py
: Fix typo when creatintg treated directory. Dark treated files are now saved undertreated/dark
.
0.7.0#
Add ewoks support instead of pypushflow and allow for batch processing (MR !143, !149)
requirements.txt
: Add ewoksorange and remove Orange3 version (MR !143, !144)Core:
dataset.py
:Accept new parameter
isH5
which reads an hdf5 file (MR !140)
dimensions.py
:Dimension
: Add_range
attribute (MR !141)Create new method
_values_with_step
that finds the range between a set of values (MR !141)Modify method
_set_unique_values
to userange
(start/stop/step) as first option for the values, and to usesize
ifstep
is 0 or None. (MR !141, !142, !144)
mapping.py
:fit
: Fix typo: useint_thresh
parameter instead of fixed value (MR !140)magnification
: Add parameter to uncenter axes (MR !151)Add function to compute peak position map and add tests (MR !150)
Add tests for moments, magnification and rsm (MR !148)
process.py
: Use ewoks instead of pypushflow and update classes as necessary (MR !143, !142)data_selection.py
: Create new function to load data and create Dataset (MR !143)tests: Use seed for random numbers to avoid failing of tests in image registration(MR !153)
Decomposition (MR !146):
Use chunks to compute norms.
Add squared frobenius norm.
NMF: Fix update of H and W matrices by chunks. Use
error_step
to check for convergence.tests: Use seed for random numbers to avoid failing of tests in NMF and NICA (MR !153)
GUI:
Pass parent by parameter when setting datasets (to all GUI widgets) and add
_updateDataset
methods to free memory of datasets (MR !140)datasetSelectionWidget.py
: Add checkbox for hdf5 files, dimension definition is still not controlled for this files (MR !140)dimensionsWidget.py
:Add
Range
vertical header (MR !141)_DimensionItem
: Create_RangeWidget
to acceptstart/stop/step
values before using unique values(MR !141)DimensionWidget
: Improvefit
method to userange
andstep
values (MR !141, !144)
grainPlotWidget.py
: Fix typo when showing kurtosis maps (MR !145)rockingCurvesWidget.py
: Fix bug when computing peak position map and add residuals map (MR !145, !150)magnificationWidget.py
: Add center axes checkbox (MR !151)
orangecontrib (MR !147):
Add
flash.py
file that containsFlashWidget
: widget to update previous datasets and free memoryUpdate orange widgets to emit
self
together with the dataset to be able to update previous datasets
0.6.1#
Downgrade pypushflow to 0.1.0 for compatibility issues (MR !137)
Core (MR !137):
dataset.py
:nica_nmf: Set ‘init’ as ‘custom’ when initializing NMF to use H and W absoulte values from NICA.
Change
cascade
towaterfall
Mosaicity only computable in two dimensions.
compute_transformation
: Flip axes if rotate is checked (MR !138)Add
Transformation
class (MR !138)
mapping.py
(MR !138):rsm: Convert to degrees and fix computation typo.
magnification: Convert to radians before computing sin and cos and add topography option.
Decomposition (MR !137):
nica.py
: Add epsilon to avoid division by 0.
GUI:
blindSourceSeparationWidget.py
: Change NNICA to NICA (MR !137)shiftCorrectionWidget.py
: Convert ‘shift’ attribute to numpy array after setter (MR !137)magnificationWidget.py
: Add topography checkbox and orientation axis combobox (MR !138)grainPlotWidget.py
&zSumWidget.py
: Rotate image 90 degrees in case of active rotation (rsm), and set label corresponding to the transformation type (if so) (MR !138)
orangecontrib (MR !137):
shiftcorrection.py
: Fix bug when clearing stack and loading and saving shift.
0.6.0#
Core:
Dataset:
Save data into hdf5 instead of numpy files, all images are saved into a single hdf5 file (MR !128):
Data
class methodsapply_funcs
andsave
are modified to work with h5py and to only replace the necessary rows of the file.DataUrls
used inDataset
are linked to the corresponding image (using data slicing of h5py).Temporary datasets are used to not lose information in case of crash or abortion.
Raise error if directory for treated data is read-only (MR !114)
Use treated data directory for dark files (MR !114)
Add
roi_dir
parameter inapply_roi
as directory path for the new dataset (MR !122)New treated files in disk automatically replace previous ones except said by parameter (MR !123)
Add
get_metadata_value
method to obtain metadata info from a key (MR !124)Add attribute
transformation
with the transformation values and methodcompute_transformation
to compute it (MR !125)Modify
find_shift
andapply_shift
methods parameters to usesteps
instead ofh_step
andh_max
and use linear shift when applying shifts greater than 1 (MR !127)Add methods
find_shift_along_dimension
andapply_shift_along_dimension
that find and apply shift, respectively, in a loop along a dimensions values (MR !134)
Mapping:
Apply median filter to COM and std to remove Nans (MR !117)
Add functions
compute_rsm
andcompute_magnification
(MR !125)
Image registration:
Modify shift detection to work with higher values of shift than 0.5 (MR !127)
Process (MR !130):
Add new process
_GrainPlot
Add new process
_Transformation
Add step and chunk properties in
_NoiseRemoval
process
ROI:
Fix typo when computing 2D ROI (MR !130)
GUI:
grainPlotWidget.py
:Orientation distribution: Increase resolution of hsv key, set coordinate labels as the angles of the motors, add checkbox to center angle values to 0 and fix bugs (MR !116)
Add export button that saves maps into Nexus file (MR !132)
Stop using opticolor (MR !117)
Modify axes if transformation is present and set global attributes origin and scale (MR !125)
rockingCurvesWidget.py
:Add two scatter points at the frame number position in the rocking curves (MR !119)
noiseRemovalWidget.py
:Fix bug when resetting data and applying new operations (MR !115)
Only show abort button if abortion is possible (MR !128)
Add step and chunks properties (MR !130)
roiWidget.py
:Return bg_dataset in
get_dataset
(MR !122)Use same directory for consecutive roi applies (MR !122)
Only show abort button if abortion is possible (MR !128)
displayComponentsWidget.py
: Set X values as motor positions when filtering by dimensions (MR !121)linkComponentsWidget.py
: Add colormap (orientation distribution maps) from the components (MR !126)Add
rsmWidget.py
for Reciprocal Space Map 1D datasets (MR !124)Add
magnificationWidget.py
for dataset with magnification values (MR !125)shiftCorrectionWidget.py
:Add
ShiftCorrectionDialog
which includesShiftCorrectionWidget
as main widget (MR !127)Add
_filtered_shift
attribute that contains the shift values, if any, along a dimension (MR !134)Use methods for finding and applying shift along a dimension in
Dataset
(MR !134)Modify checkbox to be used when shift should be applied to only selected value (MR !134)
Update values of vertical and horizontal shifts to show currently selected dimension value shift (MR !134)
Create
zSumWidget
to show plot of zsum (MR !131)
pffaddon: Add alias for
GrainPlotWidgetOW
, forTransformationWidgetOW
(MR !130) and forzSumWidgetOW
(MR !131)app: Modify
ows_to_script.py
executable script arguments for Dataset (MR !130)orangecontrib:
Add
transformation.py
that shows eithermagnificationWidget
orRSMWidget
(MR !125, MR!133)Add step and chunks Settings in
NoiseRemovalWidgetOW
(MR !130)Add local in
shiftCorrectionWidgetOW
to avoid bugs depending on the local computers locale (MR !130)Use
zSumWidget
inZSumWidgetOW
(MR !131)
0.5.0#
Add tqdm package to requirements.txt and setup.py
Core:
Dataset:
Update constructor to admit
first_filename
parameter. (MR !106)Fix reshaping: Correct the methodology used for reshaping to be consistent with the way data is obtained in id06 (MR !101)
Modify methods that work with dimensions (get_data, apply_shift) so that they work if more than one dimension is fixed (MR !102)
Add
running_data
property which contains the data currently being used by any of the operations (if any). This data is stopped in case ofAbort
option called (MR !95)apply_background_subtraction:
Use multiprocessing to chunk images (MR !87)
Add step option to compute median using only every step image (MR !87)
Add tests with step and chunks and add docstring (MR !92)
Add
apply_moments
method for computing orientation distribution and colorkey based on the dimensions (for now only works with two dimensions) (MR !96)Add
apply_fit
method for fitting the rocking curves of the data (a curve corresponds to a pixel around the stack), multiprocessing is used to chunk the images (MR !98)Add
apply_threshold
method for thresholding the data (MR !108)
Create new file
dimension.py
that contains the classes AcquisitionDims and Dimensions moved fromdataset.py
(MR !105)Create new file
mapping.py
with several functions: fit a rocking curve and computation of moments (MR !98)process.py
: Add new process_RockingCurves
(MR !104)Add
test_dimension.py
file that contains the tests that use the Dimension and AcquisitionDim classes (MR !105)
GUI:
Add setters and getters for colormaps in widgets that use them (MR !110)
Disable buttons when computing operations (MR !109)
datasetSelectionWidget.py
(MR !106)Add new tab for treated data.
Create class
DirSelectionWidget
noiseRemovalWidget.py
:Add
setDataset
method inNoiseRemovalDialog
to enable buttons after the dataset is set (MR !100)Add widgets only visible when data in disk, which give option to use step or chunks when computing the median (MR !87, MR!90)
Fix bug when showing or not the in disk widget (MR !97)
Make methods
toggleChunks
andtoggleInDiskWidget
private (MR !100)Correctly set and get properties (background, method, etc) (MR !104)
Add threshold removal option (MR !108)
Add signal that emits when method starts or ends computing (MR !109)
Fix some typos (MR !111)
shiftCorrectionWidget.py
:Use
skimage.registration.phase_correlation
instead ofregister_translation
when finding shift (MR !91)Fix bug when shifting only using first dimension (MR !99)
Round shift to 5 decimals (MR !105)
roiSelectionWidget.py
:Run ROI operation in thread and add abort button(MR !95)
blindSourceSeparationWidget.py
:Modify
Method
class so that its values are a description of the method. The keys are used in theBlindSourceSeparationWidget
as text in the combobox, and the values are its tooltips (MR !100)Remove widgets to set a maximum number of components (MR !105)
pca.py
(MR !105):Add title and labels to plot
Automatically compute PCA when creating widget and remove widgets to set a maximum number of components
displayComponentsWidget.py
:Add parameter in
setDimensions
to know the shape of the data, and use it to correctly take values from W (MR !107)
ChooseDimensionWidget
: Add as many dimension widgets as dimensions are (minus 1), so all the dimensions are fixed except for one (MR !102)Create
GrainPlotWidget
:Show different COM, FWHM, Skewness, Kurtosis of the dataset around a certain dimension (MR !96)
Add a contours map to show the contours of the orientation distribution on top of the colorkey (MR !96)
Add a plot for the mosaicity map (only works with two dimensions) (MR !96)
Create
RockingCurvesWidget
(MR !98, MR !111, MR !112):Show the stack of images where the user can click any pixel.
Show a 1D plot with the rocking curve of the pixel selected in the stack.
A ChooseDimensionWidget allows the data to be filtered by the chosen dimension.
A button to fit the data shows a plot with 3 maps computed from the fitted data: Integrated intensity, FWHM and peak position.
If data is filtered by dimensions then the data is fitted in chunks, where every chunk is a certain value of the chosen dimension.
Create
LineProfileWidget
(MR !103):Upload a
*.npy
image from disk and show intensity curve from a chosen y value of the image.
Create
ShowStackWidget
to show stack of data (MR !106)
pffaddon: Add alias for rockingCurveWidget (MR !104)
orangecontrib:
Zsum: Use
ChooseDimensionDock
instead ofChooseDimensionWidget
and fix bug when computing sum in disk (MR !92)Add
GrainPlotWidgetOW
to show aGrainPlotWidget
(MR !96)Add
RockingCurvesWidgetOW
to show aRockingCurvesWidget
(MR !98)Add
LineProfileWidgetOW
forLineProfileWidget
(MR !103)Add properties in
NoiseRemovalWidgetOW
for threshold removal (MR !108)Add colormap as input and output on widgets that use it (MR !110)
0.4.2#
Use version 4.1.2.30 of opencv to avoid uncompatibility with PyQt5 latest release
0.4.1#
Modify
setup.py
(MR !82):Add
opencv-python
,scikit-image
andsilx
ininstall_requires
.Add package
full
inextras
withmatplotlib
,PyQt5
andorange
.Add package
test
inextras
withpillow
.
Core:
dataset.py
:Add parameter bins when partitioning data in
Dataset
(MR !67)Create
in_memory
setter inDataset
(MR !68)Improve methods
flatten
,reshape
andtake
inData
(MR !67)Add try-except when fitting data in blind source separation methods to close file in case of crash (MR !71)
Add methods to convert dimensions to dictionary and viceversa in
AcquisitionDims
(MR !74)Add
to_memory
method inDataset
to load only part of the data into memory (MR !77)Add property
ndim
inData
(MR !80)
Decomposition:
Fix bug in IPCA with cases where in the last iteration the chunk was smaller than the number of components (omit last iteration) (MR !73)
GUI:
Temporarily register resources directory in when used in
DisplayComponentsWidget
(MR !84)Change colormap default normalization to
log
for better visualization of the data (MR !85)Add widget for bins in
DataPartitionWidget
(MR !67)Add parameter for chunks in
NoiseRemovalWidget
(MR !68)Add abort options in
dataPartitionWidget
,NoiseRemovalWidget
andShiftCorrectionWidget
(MR !68)Get next free axis when removing dimensions in
DimensionsWidget
(MR !86)Fix bug when clearing stack in
RoiSelectionWidget
(MR !67)Fix bug when getting filtered indices in
DataPartitionWidget
(MR !68)
IO:
New file
dataset_io.py
with functions to save and load data into/from json files (MR !74)
Orangecontrib:
Remove progressBar due to bugs in the workflows (MR !84)
Fix bug with qthreads when creating and deleting the thread using orange widgets (MR !70)
0.4.0#
Refactors the project (MR !48)
Changes default colormap to cividis.
Core:
Dataset class stops inheriting from
silx.qt.QObject
The dataset class takes control of all the operations done to the data.
Metadata is obtained from the frames using
fabioh5
from silx and then each frame is closed to spare space in memory.Creates new class
Data
that inherits from numpy.ndarray and contains the corresponding urls and metadata of the data.Adds new methods to
Dataset
for image operations, image registration, region of interest, and partition by intensity (filter data), that are applied differently depending on if the data is loaded into memory or is taken from disk in chunks.Data can be saved into an Hdf5 file with images in the rows.
Implement in
Data
methodsshape
,reshape
,flatten
,take
,__getitem__
that work similarly to a numpy.ndarray.Adds and modifies functions in
imageOperations.py
andimageRegistration.py
to be used when data is not loaded into memory.Adds class
IPCA
inblindSourceSeparation.py
that uses IncrementalPCA from scikit-learn to apply PCA in chunks.Implements methods in
Dataset
to apply blind source separation algorithms to the data.PCA and NMF algorithms used from scikit-learn when data is loaded into memory.
Decomposition:
A new package
decomposition
is created.A base class
Base
is created for decomposition methods.Adds class
NMF
that updates the matricesH
andW
using NMF method without having the data in memory.Adds class
NICA
with the already implemented algorithm incore
.Adds class
PCA
currently not used (substitued for PCA in scikit-learn).
GUI:
Modifies all widgets to only have
Dataset
objects and call its corresponding methods.
Core:
Adds method
in_memory
to Dataset to upload data from disk or remove data from memory (MR !51)Adds method that returns intensity per frame (MR !58)
Number of bins can be passed as parameter when partitioning the data by intensity (MR !52)
Fix bugs when not closing Hdf5 files (MR !56)
Adds methos
zsum
inDataset
to sum images when not in memory (MR !57)Fix bugs with
__getitem__
inData
(MR !57)
Decomposition:
Adds IPCA to decomposition package (MR !50)
NICA implements IPCA for whitening when data is not in memory. Fix bugs when computing IPCA with data in the rows or in the columns (MR !53)
Allow matrices H and W in IPCA to be stored in disk using Hdf5 (MR !54)
GUI:
Adds ComboBox in
DatasetSelectionWidget
to use data from disk or load it into memory (MR !57)Adds widget to partition the data by intensity (MR !58)
Removes ComboBox in
DatasetSelectionWidget
to filter the data (MR !59)
Orangecontrib:
Add corresponding data partition widget (MR !58)
Update example tutorial (MR !64)
0.3.0#
Adds resources package (MR !29)
Adds configuration file for default parameters (MR !30)
Minor fixes (MR !12 !14 !15 !32 !37 !41 !46)
Use silx backend when available (MR !44)
Core:
Adds tolerance to dimensions that defines the uniqueness of its values (MR !17)
Modifies ROI performance (MR !23)
Implements blind source separation algorithms (MR !18 !20 !22 !28)
Implements algorithms for linking components between datasets: ORB, SIFT, Euclidean distance (MR !36 !44 !45)
GUI:
Creates a unified noise removal widget (MR !21 !24 !25)
Adds checkbox to filter the data in
DataSelectionWidget
(MR !19)Improves
DimensionWidget
(MR !16 !17 !33)Improves
roiSelectionWidget
(MR !23 !31 !43)Implements widgets
blindSourceSeparationWidget
anddisplayComponentsWidget
to display the components (MR !18 !22 !26 !29 !35)Creates
PCAWidget
to show the eigenvalues of the PCA computation (MR !22)Creates widget
LinkComponentsWidget
that implements the component matching algorithms from two sets of components (MR !36 !38)
IO:
Creates functions for reading and writing the components of the BSS into Nexus files (MR !42)
0.2.0#
Renames project linkdick06 to darfix
Refactors project into core, gui, io and test packages
Adds unittests
Adds orangecontrib package
Adds examples package
Adds continous integration with gitlab-ci
Adds requirements.txt file with dependencies on numpy, silx, PyQt5, opencv-python, scikit-image and orange3 with version 3.22.0
Core:
Dataset class inherits from
silx.qt.QObject
Adds threshold to split data into high intensity images and low intensity images
Adds
Dimension
class to save information about how the frames are taken through the datasetAdds roi file that implements region of interest functions
Image registration operations moved to new file
imageRegistration.py
Adds shift detection using OpenCV
Adds
autofocus.py
to use at the shift detectionAdds
geneticShiftDetection
file to improve shift detection using a genetic algorithm
GUI:
Adds
RoiSelectionWidget
Adds
ShiftCorrectionWidget
to apply shift detection and shift correctionAdds widgets
BackgroundSubstractionWidget
andHotPixelRemovalWidget
for noise removalAdds widgets for data selection, metadata, and choosing dimensions
Adds a
QThread
,operationThread
, to run widgets operations in a threadAdds utils to create datasets from scratch
Removes
frameInterpretationWidget
and addsDimensionWidget
IO:
Adds utils
0.1.0#
Adds project build, documentation and test structure
Adds continuous integration set-up for Gitlab
Adds EDF reader from Fabio
Adds operations for correction of images in imageOperations
Adds notebook tutorial