From 63621067c3abd0bfb72c0b488b58ded8f1948e18 Mon Sep 17 00:00:00 2001 From: ngreenwald Date: Thu, 23 Apr 2020 20:06:05 -0700 Subject: [PATCH] simpler itertools.product --- .travis.yml | 3 +-- caliban_toolbox/reshape_data.py | 15 ++++----------- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9531bbf..d7727da 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,8 +6,7 @@ git: language: python -python: - - 3.7.1 +python: - 3.6 cache: pip diff --git a/caliban_toolbox/reshape_data.py b/caliban_toolbox/reshape_data.py index 54171e9..c6ed92d 100644 --- a/caliban_toolbox/reshape_data.py +++ b/caliban_toolbox/reshape_data.py @@ -336,8 +336,7 @@ def save_npzs_for_caliban(resized_xr, original_xr, log_data, save_dir, blank_lab os.makedirs(os.path.join(save_dir, 'separate')) # for each fov, loop through 2D crops and 3D slices - for indices in product(range(fov_len), range(num_crops), range(num_slices)): - fov, crop, slice = indices + for fov, crop, slice in product(range(fov_len), range(num_crops), range(num_slices)): # generate identifier for crop npz_id = 'fov_{}_crop_{}_slice_{}'.format(fov_names[fov], crop, slice) @@ -461,8 +460,7 @@ def load_npzs(crop_dir, log_data, verbose=True): saved_files = os.listdir(crop_dir) # for each fov, loop over each 2D crop and 3D slice - for indices in product(range(fov_len), range(num_crops), range(num_slices)): - fov, crop, slice = indices + for fov, crop, slice in product(range(fov_len), range(num_crops), range(num_slices)): # load NPZs if save_format == 'npz': npz_path = os.path.join(crop_dir, get_saved_file_path(saved_files, @@ -527,14 +525,9 @@ def stitch_crops(annotated_data, log_data): if annotated_data.shape[3] != 1: raise ValueError('Stacks must be combined before stitching can occur') - print('annotated shape: {}'.format(annotated_data.shape)) - print('num rows, num cols {} {}'.format(len(row_starts), len(col_starts))) # for each fov and stack, loop through rows and columns of crop positions - for indices in product(range(fov_len), range(stack_len), - range(len(row_starts)), range(len(col_starts))): - - fov, stack, row, col = indices - print('row, col {} {}'.format(row, col)) + for fov, stack, row, col in product(range(fov_len), range(stack_len), + range(len(row_starts)), range(len(col_starts))): # determine what crop # we're currently working on crop_counter = row * len(row_starts) + col