Fixes split calculation bug and updates setup and workflow

apasarkar · Sep 15, 2023 · 172ce41 · 172ce41
1 parent ddd56fd
commit 172ce41
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/.github/workflows/dev.yml b/.github/workflows/dev.yml
@@ -5,7 +5,7 @@ name: Python package
 
 on:
   push:
-    branches: [ "dev*"]
+    branches: [ "main"]
 
 jobs:
   build:

diff --git a/jnormcorre/motion_correction.py b/jnormcorre/motion_correction.py
@@ -83,6 +83,7 @@
 from functools import partial
 import time
 
+import random
 import multiprocessing
 
 
@@ -2720,7 +2721,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
     shape_mov = (np.prod(dims), T)
     if num_splits is not None:
         num_splits = min(num_splits, len(idxs))
-        idxs = np.array(idxs)[np.random.randint(0, len(idxs), num_splits)]
+        idxs = random.sample(idxs, num_splits)
         save_movie = False
 
     if save_movie:
@@ -2745,7 +2746,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
     pars = []
     for idx in idxs:
         logging.debug('Processing: frames: {}'.format(idx))
-        pars.append([fname, fname_tot, idx, shape_mov, template, strides, overlaps, max_shifts, np.array(
+        pars.append([fname, fname_tot, np.array(idx), shape_mov, template, strides, overlaps, max_shifts, np.array(
             add_to_movie, dtype=np.float32), max_deviation_rigid, upsample_factor_grid,
             newoverlaps, newstrides, nonneg_movie, is_fiji, var_name_hdf5, indices, filter_kernel])
 

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
     version="0.0.6",
     description="Jax-accelerated implementation of normcorre",
     packages=setuptools.find_packages(),
-    install_requires=["future","numpy", "scipy", "h5py", "tqdm", "matplotlib", "opencv-python", "tifffile", "typing", "torch", "pynwb", "pillow", "scikit-image", "jax", "jaxlib"],
+    install_requires=["future","numpy", "scipy", "h5py", "tqdm", "matplotlib", "opencv-python", "tifffile", "typing", "torch", "pynwb", "pillow", "scikit-image", "jax", "jaxlib", "pytest"],
     classifiers=(
         "Programming Language :: Python :: 3",
     ),
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,7 +5,7 @@ name: Python package @@
     on:
       push:
-        branches: [ "dev*"]
+        branches: [ "main"]
     jobs:
       build:
@@ Expand Down @@