[ENH] switch tqdm for rich progress bar (#95)

* switch tqdm for rich progress bar

* lint

* edit doc - full_test

docs/source/contributing.md

@@ -56,6 +56,9 @@ git checkout -b your_branch
 
 4. Commit your changes on this branch.
 
+If you want to make sure all the tests will be run by github continuous integration,
+make sure that your commit message contains `full_test`.
+
 5. Run the tests locally; you can run spectfic tests to speed up the process:
 
 ```bash

giga_connectome/atlas.py

@@ -3,13 +3,13 @@
 from typing import Union, List
 
 from pathlib import Path
-from tqdm import tqdm
 import nibabel as nib
 from nilearn.image import resample_to_img
 from nibabel import Nifti1Image
 from pkg_resources import resource_filename
 
 from giga_connectome.logger import gc_logger
+from giga_connectome.utils import progress_bar
 
 gc_log = gc_logger()
 
@@ -110,21 +110,30 @@ def resample_atlas_collection(
     """
     gc_log.info("Resample atlas to group grey matter mask.")
     resampled_atlases = []
-    for desc in tqdm(atlas_config["file_paths"]):
-        parcellation = atlas_config["file_paths"][desc]
-        parcellation_resampled = resample_to_img(
-            parcellation, group_mask, interpolation="nearest"
-        )
-        filename = (
-            f"tpl-{template}_"
-            f"atlas-{atlas_config['name']}_"
-            "res-dataset_"
-            f"desc-{desc}_"
-            f"{atlas_config['type']}.nii.gz"
+
+    with progress_bar(text="Resampling atlases") as progress:
+        task = progress.add_task(
+            description="resampling", total=len(atlas_config["file_paths"])
         )
-        save_path = group_mask_dir / filename
-        nib.save(parcellation_resampled, save_path)
-        resampled_atlases.append(save_path)
+
+        for desc in atlas_config["file_paths"]:
+            parcellation = atlas_config["file_paths"][desc]
+            parcellation_resampled = resample_to_img(
+                parcellation, group_mask, interpolation="nearest"
+            )
+            filename = (
+                f"tpl-{template}_"
+                f"atlas-{atlas_config['name']}_"
+                "res-dataset_"
+                f"desc-{desc}_"
+                f"{atlas_config['type']}.nii.gz"
+            )
+            save_path = group_mask_dir / filename
+            nib.save(parcellation_resampled, save_path)
+            resampled_atlases.append(save_path)
+
+        progress.update(task, advance=1)
+
     return resampled_atlases
 
 

giga_connectome/postprocess.py

@@ -2,7 +2,6 @@
 from pathlib import Path
 
 import h5py
-from tqdm import tqdm
 import numpy as np
 from nilearn.connectome import ConnectivityMeasure
 from nilearn.maskers import NiftiLabelsMasker, NiftiMapsMasker
@@ -12,6 +11,7 @@
 from giga_connectome.connectome import generate_timeseries_connectomes
 from giga_connectome.denoise import denoise_nifti_voxel
 from giga_connectome.logger import gc_logger
+from giga_connectome.utils import progress_bar
 
 gc_log = gc_logger()
 
@@ -101,53 +101,61 @@ def run_postprocessing_dataset(
     )
 
     # transform data
-    gc_log.info("Processing subject")
+    with progress_bar(text="Processing subject") as progress:
+        task = progress.add_task(
+            description="processing subject", total=len(images)
+        )
 
-    for img in tqdm(images):
-        print()
-        gc_log.info(f"Processing image:\n{img.filename}")
+        for img in images:
+            print()
+            gc_log.info(f"Processing image:\n{img.filename}")
 
-        # process timeseries
-        denoised_img = denoise_nifti_voxel(
-            strategy, group_mask, standardize, smoothing_fwhm, img.path
-        )
-        # parse file name
-        subject, session, specifier = utils.parse_bids_name(img.path)
-        for desc, masker in atlas_maskers.items():
-            attribute_name = f"{subject}_{specifier}_atlas-{atlas}_desc-{desc}"
-            if not denoised_img:
-                time_series_atlas, correlation_matrix = None, None
-
-                gc_log.info(f"{attribute_name}: no volume after scrubbing")
-
-                continue
-
-            # extract timeseries and connectomes
-            (
-                correlation_matrix,
-                time_series_atlas,
-            ) = generate_timeseries_connectomes(
-                masker,
-                denoised_img,
-                group_mask,
-                correlation_measure,
-                calculate_average_correlation,
+            # process timeseries
+            denoised_img = denoise_nifti_voxel(
+                strategy, group_mask, standardize, smoothing_fwhm, img.path
             )
-            connectomes[desc].append(correlation_matrix)
-
-            # dump to h5
-            flag = _set_file_flag(output_path)
-            with h5py.File(output_path, flag) as f:
-                group = _fetch_h5_group(f, subject, session)
-                timeseries_dset = group.create_dataset(
-                    f"{attribute_name}_timeseries", data=time_series_atlas
+            # parse file name
+            subject, session, specifier = utils.parse_bids_name(img.path)
+            for desc, masker in atlas_maskers.items():
+                attribute_name = (
+                    f"{subject}_{specifier}_atlas-{atlas}_desc-{desc}"
                 )
-                timeseries_dset.attrs["RepetitionTime"] = img.entities[
-                    "RepetitionTime"
-                ]
-                group.create_dataset(
-                    f"{attribute_name}_connectome", data=correlation_matrix
+                if not denoised_img:
+                    time_series_atlas, correlation_matrix = None, None
+
+                    gc_log.info(f"{attribute_name}: no volume after scrubbing")
+
+                    progress.update(task, advance=1)
+                    continue
+
+                # extract timeseries and connectomes
+                (
+                    correlation_matrix,
+                    time_series_atlas,
+                ) = generate_timeseries_connectomes(
+                    masker,
+                    denoised_img,
+                    group_mask,
+                    correlation_measure,
+                    calculate_average_correlation,
                 )
+                connectomes[desc].append(correlation_matrix)
+
+                # dump to h5
+                flag = _set_file_flag(output_path)
+                with h5py.File(output_path, flag) as f:
+                    group = _fetch_h5_group(f, subject, session)
+                    timeseries_dset = group.create_dataset(
+                        f"{attribute_name}_timeseries", data=time_series_atlas
+                    )
+                    timeseries_dset.attrs["RepetitionTime"] = img.entities[
+                        "RepetitionTime"
+                    ]
+                    group.create_dataset(
+                        f"{attribute_name}_connectome", data=correlation_matrix
+                    )
+
+                progress.update(task, advance=1)
 
         gc_log.info(f"Saved to:\n{output_path}")
 

giga_connectome/utils.py

@@ -4,6 +4,17 @@
 from bids.layout import Query
 from bids import BIDSLayout
 
+from rich.progress import (
+    BarColumn,
+    MofNCompleteColumn,
+    Progress,
+    SpinnerColumn,
+    TaskProgressColumn,
+    TextColumn,
+    TimeElapsedColumn,
+    TimeRemainingColumn,
+)
+
 from giga_connectome.logger import gc_logger
 
 gc_log = gc_logger()
@@ -192,3 +203,15 @@ def check_path(path: Path):
             f"Specified path already exists:\n\t{path}\n"
             "Old file will be overwritten"
         )
+
+
+def progress_bar(text: str, color: str = "green") -> Progress:
+    return Progress(
+        TextColumn(f"[{color}]{text}"),
+        SpinnerColumn("dots"),
+        TimeElapsedColumn(),
+        BarColumn(),
+        MofNCompleteColumn(),
+        TaskProgressColumn(),
+        TimeRemainingColumn(),
+    )

pyproject.toml

@@ -24,7 +24,6 @@ dependencies = [
   "nilearn >=0.10.2",
   "pybids >=0.15.0, <0.16.0",
   "templateflow < 23.0.0",
-  "tqdm",
   "setuptools",
   "jinja2 >= 2.0",
   "rich",

requirements.txt

@@ -26,7 +26,6 @@ six==1.16.0
 SQLAlchemy==1.3.24
 templateflow==0.8.1
 threadpoolctl==3.2.0
-tqdm==4.66.1
 typing_extensions==4.9.0
 tzdata==2023.3
 urllib3==2.1.0