Disabling progress bars (#2763)

* utils.py: Create sct_progress_bar

As suggested in #2724 it can be disabled by setting the
SCT_PROGRESS_BAR to no, off, or false (case insensitive)

* progress bars: replace all tqdm bars with sct_progress_bar

* sct_run_batch: Disable progress bars in batch runner

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>

scripts/msct_register.py

@@ -19,14 +19,14 @@
 import sys, os, logging
 from math import asin, cos, sin, acos
 import numpy as np
-from tqdm import tqdm
 
 from scipy import ndimage
 from scipy.signal import argrelmax, medfilt
 from scipy.io import loadmat
 from nibabel import load, Nifti1Image, save
 
 from spinalcordtoolbox.image import Image, find_zmin_zmax, spatial_crop
+from spinalcordtoolbox.utils import sct_progress_bar
 
 import sct_utils as sct
 import sct_apply_transfo
@@ -796,8 +796,8 @@ def register2d_centermassrot(fname_src, fname_dest, paramreg=None, fname_warp='w
     th_max_angle *= np.pi / 180
 
     # Loop across slices
-    for iz in tqdm(range(0, nz), unit='iter', unit_scale=False, desc="Estimate cord angle for each slice",
-                   ascii=False, ncols=100):
+    for iz in sct_progress_bar(range(0, nz), unit='iter', unit_scale=False, desc="Estimate cord angle for each slice",
+                               ascii=False, ncols=100):
         try:
             # compute PCA and get center or mass based on segmentation
             coord_src[iz], pca_src[iz], centermass_src[iz, :] = compute_pca(data_src[:, :, iz])
@@ -884,8 +884,8 @@ def register2d_centermassrot(fname_src, fname_dest, paramreg=None, fname_warp='w
     warp_inv_y = np.zeros(data_src.shape)
 
     # construct 3D warping matrix
-    for iz in tqdm(z_nonzero, unit='iter', unit_scale=False, desc="Build 3D deformation field",
-                   ascii=False, ncols=100):
+    for iz in sct_progress_bar(z_nonzero, unit='iter', unit_scale=False, desc="Build 3D deformation field",
+                               ascii=False, ncols=100):
         # get indices of x and y coordinates
         row, col = np.indices((nx, ny))
         # build 2xn array of coordinates in pixel space

scripts/sct_analyze_texture.py

@@ -17,13 +17,12 @@
 import itertools
 import argparse
 
-import tqdm
 from skimage.feature import greycomatrix, greycoprops
 
 import sct_utils as sct
 import spinalcordtoolbox.image as msct_image
 from spinalcordtoolbox.image import Image
-from spinalcordtoolbox.utils import Metavar, SmartFormatter, ActionCreateFolder
+from spinalcordtoolbox.utils import Metavar, SmartFormatter, ActionCreateFolder, sct_progress_bar
 
 def get_parser():
     # Initialize the parser
@@ -251,7 +250,7 @@ def compute_texture(self):
             dct_metric[m] = im_2save
             # dct_metric[m] = Image(self.fname_metric_lst[m])
 
-        with tqdm.tqdm() as pbar:
+        with sct_progress_bar() as pbar:
             for im_z, seg_z, zz in zip(self.dct_im_seg['im'], self.dct_im_seg['seg'], range(len(self.dct_im_seg['im']))):
                 for xx in range(im_z.shape[0]):
                     for yy in range(im_z.shape[1]):

scripts/sct_run_batch.py

@@ -122,7 +122,8 @@ def run_single(subj_dir):
         'PATH_RESULTS': path_results,
         'PATH_LOG': path_log,
         'PATH_QC': path_qc,
-        'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': str(args.itk_threads)
+        'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': str(args.itk_threads),
+        'SCT_PROGRESS_BAR': 'off'
     })
 
     # Ship the job out, merging stdout/stderr and piping to log file

spinalcordtoolbox/deepseg_sc/core.py

@@ -347,7 +347,7 @@ def segment_2d(model_fname, contrast_type, input_size, im_in):
     seg_crop = zeros_like(im_in, dtype=np.float32)
 
     data_norm = im_in.data
-    # TODO: use tqdm
+    # TODO: use sct_progress_bar
     for zz in range(im_in.dim[2]):
         # 2D CNN prediction
         pred_seg = seg_model.predict(np.expand_dims(np.expand_dims(data_norm[:, :, zz], -1), 0),
@@ -374,7 +374,7 @@ def segment_3d(model_fname, contrast_type, im_in):
     # segment the spinal cord
     z_patch_size = dct_patch_sc_3d[contrast_type]['size'][2]
     z_step_keep = list(range(0, im_in.data.shape[2], z_patch_size))
-    # TODO: use tqdm
+    # TODO: use sct_progress_bar
     for zz in z_step_keep:
         if zz == z_step_keep[-1]:  # deal with instances where the im.data.shape[2] % patch_size_z != 0
             patch_im = np.zeros(dct_patch_sc_3d[contrast_type]['size'])

spinalcordtoolbox/download.py

@@ -14,7 +14,7 @@
 import requests
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util import Retry
-from tqdm import tqdm
+from spinalcordtoolbox.utils import sct_progress_bar
 
 import spinalcordtoolbox as sct
 import spinalcordtoolbox.utils
@@ -64,15 +64,15 @@ def download_data(urls):
 
             with open(tmp_path, 'wb') as tmp_file:
                 total = int(response.headers.get('content-length', 1))
-                tqdm_bar = tqdm(total=total, unit='B', unit_scale=True, desc="Status", ascii=False, position=0)
+                sct_bar = sct_progress_bar(total=total, unit='B', unit_scale=True, desc="Status", ascii=False, position=0)
 
                 for chunk in response.iter_content(chunk_size=8192):
                     if chunk:
                         tmp_file.write(chunk)
                         dl_chunk = len(chunk)
-                        tqdm_bar.update(dl_chunk)
+                        sct_bar.update(dl_chunk)
 
-                tqdm_bar.close()
+                sct_bar.close()
             return tmp_path
 
         except Exception as e:

spinalcordtoolbox/moco.py

@@ -16,7 +16,6 @@
 import os
 from shutil import copyfile
 import glob
-from tqdm import tqdm
 import numpy as np
 import math
 import scipy.interpolate
@@ -26,6 +25,7 @@
 import csv
 
 from spinalcordtoolbox.image import Image
+from spinalcordtoolbox.utils import sct_progress_bar
 
 import sct_utils as sct
 import sct_dmri_separate_b0_and_dwi
@@ -261,8 +261,8 @@ def moco_wrapper(param):
     _, file_dwi_basename, file_dwi_ext = sct.extract_fname(file_datasub)
     # Group data
     list_file_group = []
-    for iGroup in tqdm(range(nb_groups), unit='iter', unit_scale=False, desc="Merge within groups", ascii=False,
-                       ncols=80):
+    for iGroup in sct_progress_bar(range(nb_groups), unit='iter', unit_scale=False, desc="Merge within groups", ascii=False,
+                                   ncols=80):
         # get index
         index_moco_i = group_indexes[iGroup]
         n_moco_i = len(index_moco_i)
@@ -580,8 +580,8 @@ def moco(param):
         failed_transfo = [0 for i in range(nt)]
 
         # Motion correction: Loop across T
-        for indice_index in tqdm(range(nt), unit='iter', unit_scale=False,
-                                 desc="Z=" + str(iz) + "/" + str(len(file_data_splitZ)-1), ascii=False, ncols=80):
+        for indice_index in sct_progress_bar(range(nt), unit='iter', unit_scale=False,
+                                             desc="Z=" + str(iz) + "/" + str(len(file_data_splitZ)-1), ascii=False, ncols=80):
 
             # create indices and display stuff
             it = index[indice_index]

spinalcordtoolbox/process_seg.py

@@ -8,14 +8,14 @@
 import platform
 import numpy as np
 from skimage import measure, transform
-from tqdm import tqdm
 import logging
 import nibabel
 
 from spinalcordtoolbox.image import Image
 from spinalcordtoolbox.aggregate_slicewise import Metric
 from spinalcordtoolbox.centerline.core import ParamCenterline, get_centerline
 from spinalcordtoolbox.resampling import resample_nib
+from spinalcordtoolbox.utils import sct_progress_bar
 
 
 def compute_shape(segmentation, angle_correction=True, param_centerline=None, verbose=1):
@@ -67,8 +67,8 @@ def compute_shape(segmentation, angle_correction=True, param_centerline=None, ve
         _, arr_ctl, arr_ctl_der, fit_results = get_centerline(im_segr, param=param_centerline, verbose=verbose)
 
     # Loop across z and compute shape analysis
-    for iz in tqdm(range(min_z_index, max_z_index + 1), unit='iter', unit_scale=False, desc="Compute shape analysis",
-                   ascii=True, ncols=80):
+    for iz in sct_progress_bar(range(min_z_index, max_z_index + 1), unit='iter', unit_scale=False, desc="Compute shape analysis",
+                               ascii=True, ncols=80):
         # Extract 2D patch
         current_patch = im_segr.data[:, :, iz]
         if angle_correction:

spinalcordtoolbox/straightening.py

@@ -11,13 +11,13 @@
 import os, time, logging, inspect
 import bisect
 import numpy as np
-from tqdm import tqdm
 from nibabel import Nifti1Image, save
 
 from spinalcordtoolbox.types import Centerline
 import spinalcordtoolbox.image as msct_image
 from spinalcordtoolbox.image import Image
 from spinalcordtoolbox.centerline.core import ParamCenterline, get_centerline
+from spinalcordtoolbox.utils import sct_progress_bar
 
 import sct_utils as sct
 from sct_image import pad_image
@@ -436,7 +436,7 @@ def straighten(self):
         # sct.printv(nx * ny * nz, nx_s * ny_s * nz_s)
 
         if self.curved2straight:
-            for u in tqdm(range(nz_s)):
+            for u in sct_progress_bar(range(nz_s)):
                 x_s, y_s, z_s = np.mgrid[0:nx_s, 0:ny_s, u:u + 1]
                 indexes_straight = np.array(list(zip(x_s.ravel(), y_s.ravel(), z_s.ravel())))
                 physical_coordinates_straight = image_centerline_straight.transfo_pix2phys(indexes_straight)
@@ -465,7 +465,7 @@ def straighten(self):
                     = -displacements_straight
 
         if self.straight2curved:
-            for u in tqdm(range(nz)):
+            for u in sct_progress_bar(range(nz)):
                 x, y, z = np.mgrid[0:nx, 0:ny, u:u + 1]
                 indexes = np.array(list(zip(x.ravel(), y.ravel(), z.ravel())))
                 physical_coordinates = image_centerline_pad.transfo_pix2phys(indexes)

spinalcordtoolbox/utils.py

@@ -12,6 +12,7 @@
 import argparse
 import subprocess
 import shutil
+import tqdm
 from enum import Enum
 
 logger = logging.getLogger(__name__)
@@ -386,6 +387,16 @@ def _version_string():
         return "{install_type}-{sct_branch}-{sct_commit}".format(**locals())
 
 
+def sct_progress_bar(*args, **kwargs):
+    """Thin wrapper around `tqdm.tqdm` which checks `SCT_PROGRESS_BAR` muffling the progress
+       bar if the user sets it to `no`, `off`, or `false` (case insensitive)."""
+    do_pb = os.environ.get('SCT_PROGRESS_BAR', 'yes')
+    if do_pb.lower() in ['off', 'no', 'false']:
+        kwargs['disable'] = True
+
+    return tqdm.tqdm(*args, **kwargs)
+
+
 __sct_dir__ = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 __version__ = _version_string()
 __data_dir__ = os.path.join(__sct_dir__, 'data')