Nix export of tracking results #1068

jgrewe · 2022-12-04T11:57:27Z

Description

Dear SLEAP team, thanks for developing sleap. This pr

adds an option to export analysis results to hdf5 files according to the NIX format.
makes inference.py usable from custom code line by simply passing the args to main.

For 1 I added a new NixAdaptor class in sleep.ioand support using it from the GUI as well as the convert CLI.
Reading nix-exported files works nicely using either the generic nixio python package or via the more domain specific nixtrack package (work in progress). Exporting to NIX is fully optional, the option is not even offered in the file export dialog if nixio is not installed in the environment. Hence, nixio is not added to the requirements.

Types of changes

Does this address any currently open issues?

no

Outside contributors checklist

Review the guidelines for contributing to this repository
Read and sign the CLA and add yourself to the authors list
Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
Add tests that prove your fix is effective or that your feature works
Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

❤️

codecov · 2022-12-05T18:03:53Z

Codecov Report

Merging #1068 (d1f251f) into develop (67c6da6) will increase coverage by 0.25%.
The diff coverage is 89.00%.

@@             Coverage Diff             @@
##           develop    #1068      +/-   ##
===========================================
+ Coverage    69.94%   70.19%   +0.25%     
===========================================
  Files          130      131       +1     
  Lines        22496    22751     +255     
===========================================
+ Hits         15735    15971     +236     
- Misses        6761     6780      +19

Impacted Files	Coverage Δ
sleap/gui/commands.py	`58.97% <29.16%> (-0.11%)`	⬇️
sleap/io/convert.py	`81.81% <85.18%> (-1.86%)`	⬇️
sleap/io/format/nix.py	`95.55% <95.55%> (ø)`
sleap/info/write_tracking_h5.py	`90.90% <100.00%> (+0.15%)`	⬆️
sleap/nn/inference.py	`80.07% <100.00%> (ø)`
sleap/io/video.py	`91.56% <0.00%> (+0.15%)`	⬆️

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roomrys

Thanks for creating the adaptor. I know this PR is still listed as a draft, but I had a few comments. We will also need to add a test in test_formats.py. I really like that you kept nix as an optional import. Let me know if there's anything I can help with.

sleap/gui/commands.py

sleap/io/format/nix.py

sleap/io/convert.py

roomrys

There is a vulnerability in how the track_map and skeleton_map are defined.

The track_map is a bigger concern as tracks often use non-unique names and are instead identified by the object reference. Another way of identifying Tracks is by their index in the Labels.tracks list.

The comments pertaining to skeleton_map are less critical as SLEAP does not currently support multi-Skeleton projects (although we have some infrastructure written to scale SLEAP in that direction). Like Tracks, Skeletons are not required to have unique names and can instead be identified by the object's index in Labels.skeletons.

Thanks again for creating the adaptor (and writing a test)! Let me know if there is anything I can help with.

dev_requirements.txt

sleap/io/format/nix.py

roomrys · 2022-12-14T21:29:45Z

sleap/io/format/nix.py

+    def can_write_filename(cls, filename: str) -> bool:
+        """Returns whether this adaptor can write format of this filename."""
+        raise NotImplementedError


A problem we have run into is people trying to handle .pkg.slps as .slps. Can we add a quick check here to check that the file ends in .slp instead of .pkg.slp? While the .pkg.slp contains all the pose information, the references to the videos are stored within the actual .pkg.slp and no longer reference the original video - this would result in an inaccurate nix file.

Not sure, I follow. I understood this method as checking whether or not the adaptor can write to a file with the specified extension. The sleap_analysis adaptor seems to delegate to the respective function in adaptor.py that does this.

You're right, I double checked this and was interpreting it the wrong way (i.e. filename being the name of the loaded labels object to convert). No action needed.

sleap/io/format/nix.py

roomrys · 2022-12-14T21:42:44Z

sleap/io/format/nix.py

+        def skeleton_map(source: Labels):
+            skel_map = {}
+            for s in source.skeletons:
+                if s.name in skel_map:
+                    continue
+                skel_map[s.name] = len(skel_map)
+            return skel_map
+
+        def node_map(source: Labels):
+            n_map = {}
+            for skeleton in source.skeletons:
+                for n in skeleton.nodes:
+                    if n.name in n_map:
+                        continue
+                    n_map[n.name] = len(n_map)
+            return n_map


Seeing as you only keep skeletons with unique names

if s.name in skel_map: continue

should we also only be considering the nodes of skeletons that are listed in skel_map?

I changed this to work with skeletons that are not unique regarding their name only. Nodes now also store the skeleton they are part of, if they are part of one. Accepting now all nodes irrespective of their assignment to a skeleton

roomrys · 2022-12-14T21:50:27Z

sleap/io/format/nix.py

+            for t in source.tracks:
+                if t.name in track_map:
+                    continue
+                track_map[t.name] = len(track_map)


While we hope that users will uniquely label their Tracks, it is not a requirement. Assuming the name is the unique identifier could lead to a lot of missed data.

roomrys · 2022-12-14T22:29:29Z

sleap/io/format/nix.py

+                    if inst.track is not None:
+                        track[index] = track_map[inst.track.name]
+                    else:
+                        track[index] = -1
+                    skeleton[index] = skeleton_map[inst.skeleton.name]


Based on the way track_map was created (assuming Track.name is a unique identifier), it is possible that inst.track.name is not in the track_map. Likewise for skeleton_map.

roomrys · 2022-12-14T22:42:09Z

sleap/io/format/nix.py

+                    fnames = set([n.name for n in inst.nodes])
+                    nnames = set(list(node_map.keys()))
+                    missing = nnames.difference(fnames)
+
+                    for n, p in zip(inst.nodes, inst.points):
+                        positions[index, :, node_map[n.name]] = np.array([p.x, p.y])
+                    for m in missing:
+                        positions[index, :, node_map[m]] = np.array([np.nan, np.nan])


Flagging this because bit of code assumes that all the nodes used by inst are listed in node_map. No action required, just ensure node_map continues to contain all Nodes from any Skeleton used in the project.

good catch! Since we now store all nodes whether or not they are part of a skeleton, this should no longer be an issue.

roomrys

I know you haven't re-requested a review yet, but I peaked and...

The dictionary maps are looking great! Two main concerns:

Open reference and writing to file outside of try/except (or with open ___as __)
Changing Skeleton.__eq__ behavior

roomrys · 2022-12-22T21:15:53Z

sleap/nn/inference.py

-        dists = tf.sqrt(tf.reduce_sum(tf.math.square(dists), axis=-1))  # reduce over xy
+        dists = tf.sqrt(tf.reduce_sum(dists**2, axis=-1))  # reduce over xy


Local black reformats this to to dists**2, but then Github Actions' black expects it as dists ** 2. So I just changed it to tf.math.square to get rid of this annoying miscommunication between the linters.

Suggested change

dists = tf.sqrt(tf.reduce_sum(tf.math.square(dists), axis=-1)) # reduce over xy

dists = tf.sqrt(tf.reduce_sum(dists**2, axis=-1)) # reduce over xy

dists = tf.sqrt(tf.reduce_sum(tf.math.square(dists), axis=-1)) # reduce over xy

roomrys · 2022-12-22T21:19:05Z

dev_requirements.txt

+click==8.0.4
+nixio>=1.5.3


Remove, no need to add if already in requirements.txt

roomrys · 2022-12-22T21:28:44Z

sleap/skeleton.py

+    def __eq__(self, other):
+        if not isinstance(other, Skeleton):
+            return False
+        return self.name == other.name
+


Remove this method. There are already countless SLEAP projects out there with same-name skeletons which are not equal to each other... For equality, use the Skeleton.matches method instead

https://github.com/jgrewe/sleap/blob/b3a34cc94a6fdac672eadcb944bcd94094d5747c/sleap/skeleton.py#L143-L169

I may have missed it, but do you use the == on Skeleton in your PR?

This is actually something I wanted to ask. Tried to use matches instead but got an error saying that other does not have a _graph member.
It is in the dictionaries, that the eq is needed. My first attempt was to implement __eq__ by calling matches.

sorry, my bad, apparently cannot reproduce my issue anymore, removed the __eq__

roomrys · 2022-12-22T21:40:35Z

sleap/io/format/nix.py

+        nix_file = create_file(filename, source_path, video)
+        write_data(nix_file.blocks[0], source_object, video)
+        try:
+            print(" done")
+        except Exception as e:
+            print(f"\n\t Writing failed with error message {e}!")
+        finally:
+            nix_file.close()


It might be safer to have all these lines in the try block:

try: nix_file = create_file(filename, source_path, video) write_data(nix_file.blocks[0], source_object, video) print(" done")

but that assumes that no error occurred in the create_file function and a nix_file was returned. So maybe something like this:

Suggested change

nix_file = create_file(filename, source_path, video)

write_data(nix_file.blocks[0], source_object, video)

try:

print(" done")

except Exception as e:

print(f"\n\t Writing failed with error message {e}!")

finally:

nix_file.close()

nix_file = None

try:

nix_file = create_file(filename, source_path, video)

write_data(nix_file.blocks[0], source_object, video)

print(" done")

except Exception as e:

print(f"\n\t Writing failed with error message {e}!")

finally:

if nix_file is not None:

nix_file.close()

or something else that safely closes the file while references are open.

good catch, moved the write outside the try for testing, will go into the try again.

sleap/skeleton.py

sleap/io/format/nix.py

jgrewe · 2023-01-03T09:24:53Z

@roomrys ready for review again, I guess. Thank you for your comments!
Just in case the linter fails: Running black, version 21.6b0 locally reports that files not affected by my changes would be reformatted. setup.py, docs/utils.py, docs/make_api_doctree.py. I'd rather not touch them

talmo

Hi! Jumping in here with a review since this seems almost done.

Just requested some minor changes.

Nix seems like a really cool project btw! Have you guys interacted with NWB at all?

talmo · 2023-01-06T05:59:20Z

dev_requirements.txt

Do we need to pin click to a specific version? It's a pretty common dependency which might break others so we'd rather not pin it unless necessary (or at a minimum use a more permissive version fence like click>=8.0.4,<9.0.0).

Also this should probably be in requirements.txt not dev_requirements.txt.

the click requirement was not added by me. At some point I added nixio to the dev_requirements for the tests to pass during the CI checks. I guess I left the line-break when removing nixio again, reverted to the state without line-break

Nix seems like a really cool project btw! Have you guys interacted with NWB at all?

Thanks, and yes we have been in touch with them and before NWB version 1, NIX was one of the candidate formats to be used. The NIX data model is very generic and that makes it harder to read than domain specific names for the data structures you want to store. Otoh, it keeps the number of different structures low. Eventually, NWB decided to go a slightly different way ...

We specified the version of click in dev_requirements when it broke the linting workflow in github actions. Off the topic of this PR, but I can check if we can remove the versioning now that a new release of click is out (>8.1.0).

sleap/gui/commands.py

sleap/io/format/nix.py

sleap/skeleton.py

sleap/io/convert.py

…e form scripts

…s export

not sure why this occurred. The nix adaptor cannot save instances that are not related to a frame.

make Node.name and Node.weight instance variables instead of class variables

allow for non-unique entries in node, track and skeleton. Extend node map to store the skeleton it is part of

Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

roomrys

Looks good to me. I am making the change in my comment, and then we will be good to merge.

sleap/io/format/nix.py

jgrewe · 2023-01-11T20:32:18Z

@roomrys thanks a lot for all your work on sleap and this PR. it would be totally fine with me if you decide to squash it. It has grown to be quite a few commits ;)

talmo

LGTM!

roomrys · 2023-01-20T02:17:14Z

Feeling confident we covered our basis. Changes since last review:

add tests in two more spots,
generalize the print statement to the previous export prints,
skip creating analysis files for videos that do not have any labeled frames
add documentation to cli.md

* GUI Training: Use hidden params from loaded config (#1053) * Add optional unragging arg to model export (#1054) * Fix config option to `split_by_inds` (#1060) * Convert training, validation, and test to Labels object * Add test for split_by_inds * Use Labels.extract instead of Labels(List[LabeledFrames]) * Tracking: robust assignment of the best score to an instance (#1062) * Set max instances for top down models (#1070) * Add optional unragging arg to model export * Add option to set max instances for multi-instance models * Fix test * Don't create instances during inference if no points were found (#1073) * Don't create instances during inference if no points were found * Add points check for all predictors * Fix single instance predictor logic and test * Add tests for all predictors Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> * Add one-line fix to VideoWriterSkyvideo (#1082) * Fix parser for sleap-export (#1085) * Refactor commands to load project as `AppCommand`s (#1098) * Add working Proof of Concept * Create command class for loading project * Split `LoadProjectFile` as a subclass of `LoadLabelsObject` * Reroute last existing reference * Remove debugging code * Flexibly resize input layer of `tf.keras.Model` upon loading trained model (#1084) * Add initial implementation (auto output stride problematic) * Add to load_predictor test (error when auto-compute output stride) * Use output stride from config instead of auto-computing * Fix output-stride/padding modulo error and do not resize on export * Fix resizing bug in multi-class predictors * Non-functional clean-up * Rename new input layer to original name * Add inference integration test * Minimize config surgery, generalize layer iteration Co-authored-by: Talmo Pereira <talmo@salk.edu> * Add Option to Make Trail Shade Darker/Lighter (#1103) * Make trails 60% darker than track color * Add menu option for shade of trails * Remove unexpected indent (fat-fingered) * Create signal that updates plot instead of removing and replotting items (#1134) * Create signal that updates plot instead of redrawing * Remove debug code * Non-functional self-review changes * Fix symmetric skeletons (via table input) (#1136) Ensure variable initialized before calling it * Nix export of tracking results (#1068) * [io] export tracking results to NIX file * [io] nix added to export filter only if available * [nixio] refactor, add scores link data as mtag * [nixio] speeding up export by chunked writing * [nixio] rename point score to node score * [nixio] fix missing dimension descriptor for node scores * [export analysis] support multiple formats also for bulk export * [nixio] export centroid, some documentation * [nixio] fix double dot before filename suffix * [nixio] fix bug when not all nodes were found * [nixio] housekeeping * [nix] add nix analyis output format to convert * [nix] tiny fix, catch file write error and properly close file * [inference] main takes optional args. Can be imported to run inference form scripts * [convert] simplify if else structure and outfile handling for analysis export * [nix] use pathlib instead of os * [nix] catch if there are instances with a None frame_idx ... not sure why this occurred. The nix adaptor cannot save instances that are not related to a frame. * [nix] move checks to top of write function * [nix] use absolute imports * [nix] use black to reformat * [commands] revert qtpy import and apply code style * [convert] use absolute imports, apply code style * [commands]fix imports * [inference/nix]fix linter complaint, adjust nix types for scores * [nix] add test case for nix export format * [nix] extended testing, some modifications of adaptor * [skeleton] add __eq__ to Skeleton ... make Node.name and Node.weight instance variables instead of class variables * [nix] add nixio to requirements, remove unused nix_available, ... allow for non-unique entries in node, track and skeleton. Extend node map to store the skeleton it is part of * [nix] make the linter happy * [Node] force definition of a name Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [nix] use getattr for getting grayscale information Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [nix] fixes according to review * [convert] break out of loop upon finding the video Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [commands.py] use pathilb instead of splitting filename Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [dev requirements] remove linebreak at last line * [skeleton] revert attribute creation back to original * [nix] break lines in class documentation * Ensure all file references are closed * Make the linter happy * Add tests for ExportAnalysis and (docs for) sleap-convert Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Fix body vs symmetry subgraph filtering (#1142) Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Handle changing backbones in training editor GUI (#1140) Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Added scaling functionality for both the instances and bounding box. (#1133) * Create VisibleBoundingBox class. * Added instance scaling functionality in addition to bounding box scaling functionality. * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Added new testing for scaling operation and simplified VisibleBoundingBox class code. * Added type hinting to the scaling padding and removed erroneous bounding rect initialization. Co-authored-by: Talmo Pereira <talmo@salk.edu> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Add better error message for top down (#1121) * Add better error message for top down * Add test for error message * Raise different error, fix test * Hotfix for video save #1098 (#1148) * Add a hotfix for #1098 * WIP: Add test for detecting changes on load * Finialize change on load test * Remove unused imports * Skip test if on windows since files are being used in parallel * Add central padding to SizeMatcher (#1129) * add center padding to size matcher * add test for center padding * add ensure_float option to inference layer * reformat resizing and test_resizing * Remove redundant operation * Replace existing constants with fixtures --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Added MoveNet as an external model reference (#1141) * add center padding to size matcher * add test for center padding * add ensure_float option to inference layer * reformat resizing and test_resizing * add MoveNet as an external model inference * add the movenet to the from_model_paths * add tests * add comments to movenet predictor * add tensorflow_hub to the requirements.txt * modified default video path * resolved most of the comments except expanding the predictor * expanded Predictor.from_model_paths function to include any pre-trained models. * add test_load_model * added from_trained_models in class Predictor and modified test_load_model for it. * modified test_load_model to be more generalized. * moved pretrained model from Predictor.from_trained_model to Predictor.from_model_paths and added a test for it. * Fix Predictor.from_model_paths and tests * Rename load_movenet_model to make_model_movenet * minor clean-up * Remove redundant operation * Replace existing constants with fixtures * Handle loading movenet models via load_model API * Clean-up doc strings --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Resumable Training (#1130) * add resume training functionality * add testing function for resume training functionality * linting black * Resumable Training 2 - CLI Options (#1131) * add cli options for resumable training * add test for cli resume training * black linting for cli resumable training * simplify resumable checkpoint CLI fn to a single CLI arg (#1132) * simplify resumable checkpoint CLI fn to a single CLI arg * Adam/resumable training 3 (#1150) * correct path of labels_path for test_training * add resume training to gui * add train from scratch message * Add finishing touches to resumable training PR (#1150) (#1168) * Refactor/update 'use trained' and 'resume training' checkbox logic * Simplify checkbox logic and reset model field when resume training * Reset checkboxes upon changing config selection * Handle case for updating TrainingEditor when sender is not a checkbox * Add complete state space GUI test for checkboxes * Finish combobox test * Test that form is reset * Remove straggling TODO --------- Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> Co-authored-by: jimzers <jimzersml@gmail.com> --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Return trainer from sleap-train and check that trainer configured correctly * Add CLI documentation for website --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Small (final?) revisions and fix test * Revert changes to fixture --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * GenericTableModel/View improvements (#1163) * [dataviews] GenericTableModel/View improvements ... * GenericTableView got a new argument specifying whether the ellipsis for long cell content should be right (old behavior, default) or left useful for long content such as the filenames in the video table. * GenericTableView uses all the space that available to the table. * The model's data function returns the full cell content to be shown as tool tip text. * [gui/app] set the ellipsis to be on the left for long table contents --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Add Skeleton Templates (#1122) * Update docs: change 'M1' to 'Apple Silicon' (#1188) * Bump to 1.3.0a0 (#1189) --------- Co-authored-by: sheridana <asheridan@salk.edu> Co-authored-by: getzze <getzze@gmail.com> Co-authored-by: Talmo Pereira <talmo@salk.edu> Co-authored-by: Jan Grewe <jngrewe@googlemail.com> Co-authored-by: Sean Afshar <84047864+sean-afshar@users.noreply.github.com> Co-authored-by: Jiaying Hsu <72051972+jiayinghsu@users.noreply.github.com> Co-authored-by: Adam Lee <38634441+jimzers@users.noreply.github.com> Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Jan Grewe <jan.grewe@g-node.org> Co-authored-by: Aaditya Prasad <78439225+aaprasad@users.noreply.github.com>

roomrys requested changes Dec 5, 2022

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jgrewe force-pushed the nix branch from c110137 to 7c04ca3 Compare December 9, 2022 09:12

jgrewe marked this pull request as ready for review December 9, 2022 09:21

jgrewe requested a review from roomrys December 14, 2022 17:30

roomrys requested changes Dec 14, 2022

View reviewed changes

jgrewe force-pushed the nix branch from 4f696dc to b3a34cc Compare December 22, 2022 10:07

roomrys requested changes Dec 22, 2022

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talmo requested changes Jan 6, 2023

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jgrewe added 20 commits January 10, 2023 17:44

[io] export tracking results to NIX file

0f0b64d

[io] nix added to export filter only if available

d745803

[nixio] refactor, add scores link data as mtag

0cfa562

[nixio] speeding up export by chunked writing

b934553

[nixio] rename point score to node score

610bfd6

[nixio] fix missing dimension descriptor for node scores

73692d3

[export analysis] support multiple formats also for bulk export

4559490

[nixio] export centroid, some documentation

534d079

[nixio] fix double dot before filename suffix

ad6b227

[nixio] fix bug when not all nodes were found

2dd93fa

[nixio] housekeeping

ce4880f

[nix] add nix analyis output format to convert

07f15c0

[nix] tiny fix, catch file write error and properly close file

cd0daf7

[inference] main takes optional args. Can be imported to run inferenc…

9aec920

…e form scripts

[convert] simplify if else structure and outfile handling for analysi…

9d848fd

…s export

[nix] use pathlib instead of os

105887d

[nix] catch if there are instances with a None frame_idx ...

660269f

not sure why this occurred. The nix adaptor cannot save instances that are not related to a frame.

[nix] move checks to top of write function

1a61caf

[nix] use absolute imports

32a82e7

[nix] use black to reformat

91ca722

jgrewe and others added 13 commits January 10, 2023 17:46

[inference/nix]fix linter complaint, adjust nix types for scores

80637c0

[nix] add test case for nix export format

9f23323

[nix] extended testing, some modifications of adaptor

f16fe8c

[skeleton] add __eq__ to Skeleton ...

f331431

make Node.name and Node.weight instance variables instead of class variables

[nix] add nixio to requirements, remove unused nix_available, ...

764c31c

allow for non-unique entries in node, track and skeleton. Extend node map to store the skeleton it is part of

[nix] make the linter happy

d7b8a41

[Node] force definition of a name

ec5b87c

Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

[nix] use getattr for getting grayscale information

f432ed6

Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

[nix] fixes according to review

8f8e2b2

[convert] break out of loop upon finding the video

1a0350d

Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

[commands.py] use pathilb instead of splitting filename

234c143

Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

[dev requirements] remove linebreak at last line

41eaffb

[skeleton] revert attribute creation back to original

fa125e6

jgrewe force-pushed the nix branch from e20a617 to 0884e06 Compare January 10, 2023 16:47

[nix] break lines in class documentation

849ca23

jgrewe force-pushed the nix branch from 0884e06 to 849ca23 Compare January 10, 2023 16:50

roomrys approved these changes Jan 11, 2023

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roomrys added 2 commits January 11, 2023 11:56

Ensure all file references are closed

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Make the linter happy

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Merge branch 'develop' into nix

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talmo approved these changes Jan 19, 2023

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roomrys added 3 commits January 19, 2023 11:11

Merge branch 'develop' into nix

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Add tests for ExportAnalysis and (docs for) sleap-convert

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Merge branch 'develop' into nix

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roomrys merged commit b660e00 into talmolab:develop Jan 20, 2023

jgrewe deleted the nix branch February 1, 2023 09:33

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Nix export of tracking results #1068

Nix export of tracking results #1068

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		dists = tf.sqrt(tf.reduce_sum(tf.math.square(dists), axis=-1)) # reduce over xy
		dists = tf.sqrt(tf.reduce_sum(dists**2, axis=-1)) # reduce over xy

		click==8.0.4
		nixio>=1.5.3

Nix export of tracking results #1068

Nix export of tracking results #1068

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jgrewe commented Dec 4, 2022

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