soft-matter / soft-matter/trackpy

TQDM status viewer comment

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Dominant language
Python
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Forks
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Description

I wanted to mention another status option. I've been using TQDM in linking.py for a few months now with no issues, it is most help when supplied with the number of frames in the pred_link_df_iter) call. TQDM provides an estimate for time of completion.

The console view during tracking
track: 1%|3 | 11/766 [00:00<00:54, 13.96it/s]C

from tqdm import tqdm

around line 615
def link_df_iter(features, search_range, memory=0,
            neighbor_strategy='KDTree', link_strategy='auto',
            predictor=None, adaptive_stop=None, adaptive_step=0.95,
            diagnostics=False, pos_columns=None,
            t_column=None, hash_size=None, box_size=None,
            verify_integrity=True, retain_index=False, number_of_frames=0):

around line 720
    for labeled_level, source_features, old_index in tqdm(zip(
            labeled_levels, features_forpost, index_iter),
            desc='track',total=number_of_frames):

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in linking.py at link_df_iter around the referenced lines and review the existing tqdm loop and number_of_frames parameter. Clarify the intended status-viewer behavior, then verify that the completed change provides the requested tracking progress output without disrupting link_df_iter.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Feature
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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