From 6f8ca9654ccbc5b62655b59584c2fb5048fac649 Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Tue, 8 Apr 2025 17:13:42 +0200 Subject: [PATCH 1/6] Add full path to BDV classes and trackmate methods --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a471164..2146949 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,8 +63,8 @@ detailed information, please refer to the updated API documentation. * New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related functions: * New classes: - * `ProcessingOptions` to store all options on how to process the dataset. - * `DefinitionOptions` to store all options on how to define the dataset. + * `imcflibs.imagej.bdv.ProcessingOptions` to store all options on how to process the dataset. + * `imcflibs.imagej.bdv.DefinitionOptions` to store all options on how to define the dataset. * `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the acitt input selection. * `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed @@ -94,7 +94,7 @@ detailed information, please refer to the updated API documentation. * New `imcflibs.imagej.trackmate` submodule to provide helper functions to interface with Trackmate: * Multiple functions to set up Trackmate settings with different detectors, - such as `cellpose`, `StarDist` or a `log detector`. + such as `imcflibs.imagej.trackmate.cellpose_detector`, `imcflibs.imagej.trackmate.stardist_detector` or a `imcflibs.imagej.trackmate.log_detector`. * `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity. From 758d7e205a89075013aa600a0bd186a616af1b7e Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Tue, 8 Apr 2025 17:13:57 +0200 Subject: [PATCH 2/6] Add modification to `listdir_matching` --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2146949..c84004e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,7 +76,7 @@ detailed information, please refer to the updated API documentation. Dataset" using the "Manual Loader" option. * `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it compatible with BigDataViewer/BigStitcher. - * `imcflibs.imagej.bdv.flip_axes` tocall BigStitcher's "Flip Axes" command. + * `imcflibs.imagej.bdv.flip_axes` to call BigStitcher's "Flip Axes" command. * `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to calculate pairwise shifts using Phase Correlation. * `imcflibs.imagej.bdv.filter_pairwise_shifts` for filtering pairwise shifts @@ -158,6 +158,12 @@ detailed information, please refer to the updated API documentation. * `imcflibs.imagej.projections.project_stack` to project along a defined axis using the given projection type. + +### Changed + +* `imcflibs.listdir_matching` changed to be able to use regex patterns for + matching. The regex pattern is passed as a string and the function will + return a list of all files matching the regex pattern. ## 1.4.0 From 3634ffe42eca1dee8b9a23162aaea33f92306ca5 Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Tue, 8 Apr 2025 17:18:39 +0200 Subject: [PATCH 3/6] Add changes to `calculate_mean_and_stdv` --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c84004e..a459cdf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -164,6 +164,7 @@ detailed information, please refer to the updated API documentation. * `imcflibs.listdir_matching` changed to be able to use regex patterns for matching. The regex pattern is passed as a string and the function will return a list of all files matching the regex pattern. +* `imcflibs.imagej.misc.calculate_mean_and_stdv` to allow for rounding the results. ## 1.4.0 From d55e777176ea44a4ee642e5a1283986a429312e4 Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 18:41:56 +0200 Subject: [PATCH 4/6] Fix function path --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a459cdf..07ddeb0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -161,8 +161,8 @@ detailed information, please refer to the updated API documentation. ### Changed -* `imcflibs.listdir_matching` changed to be able to use regex patterns for - matching. The regex pattern is passed as a string and the function will +* `imcflibs.pathtools.listdir_matching` changed to be able to use regex patterns + for matching. The regex pattern is passed as a string and the function will return a list of all files matching the regex pattern. * `imcflibs.imagej.misc.calculate_mean_and_stdv` to allow for rounding the results. From c99e01fbe6bb4701fdd1764d8633d20b7903c6ca Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 18:42:05 +0200 Subject: [PATCH 5/6] Newline --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07ddeb0..9f5fe53 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -158,7 +158,7 @@ detailed information, please refer to the updated API documentation. * `imcflibs.imagej.projections.project_stack` to project along a defined axis using the given projection type. - + ### Changed * `imcflibs.pathtools.listdir_matching` changed to be able to use regex patterns From df74f8995dcbdae30d987e141392b90e8e6436df Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 18:47:21 +0200 Subject: [PATCH 6/6] Modify description of the `regex` parameter --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f5fe53..b776347 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -161,9 +161,9 @@ detailed information, please refer to the updated API documentation. ### Changed -* `imcflibs.pathtools.listdir_matching` changed to be able to use regex patterns - for matching. The regex pattern is passed as a string and the function will - return a list of all files matching the regex pattern. +* `imcflibs.pathtools.listdir_matching` now has an additional optional boolean + parameter `regex` to request the parameter `suffix` being interpreted as a + regular expression for filtering. * `imcflibs.imagej.misc.calculate_mean_and_stdv` to allow for rounding the results. ## 1.4.0