Merge pull request #254 from saskra/lold_branch

Enable look_one_level_down during training as well

cellpose/__main__.py

@@ -1,5 +1,6 @@
 import sys, os, argparse, glob, pathlib, time
 import subprocess
+
 import numpy as np
 from natsort import natsorted
 from tqdm import tqdm
@@ -22,6 +23,7 @@
 import logging
 logger = logging.getLogger(__name__)
 
+
 def main():
 
     parser = argparse.ArgumentParser(description='cellpose parameters')
@@ -213,7 +215,7 @@ def main():
                 szmean = 30.
 
             test_dir = None if len(args.test_dir)==0 else args.test_dir
-            output = io.load_train_test_data(args.dir, test_dir, imf, args.mask_filter, args.unet)
+            output = io.load_train_test_data(args.dir, test_dir, imf, args.mask_filter, args.unet, args.look_one_level_down)
             images, labels, image_names, test_images, test_labels, image_names_test = output
 
             # training with all channels

cellpose/io.py

@@ -145,8 +145,8 @@ def get_label_files(image_names, mask_filter, imf=None):
     return label_names, flow_names
 
 
-def load_train_test_data(train_dir, test_dir=None, image_filter=None, mask_filter='_masks', unet=False):
-    image_names = get_image_files(train_dir, mask_filter, imf=image_filter)
+def load_train_test_data(train_dir, test_dir=None, image_filter=None, mask_filter='_masks', unet=False, look_one_level_down=True):
+    image_names = get_image_files(train_dir, mask_filter, image_filter, look_one_level_down)
     nimg = len(image_names)
     images = [imread(image_names[n]) for n in range(nimg)]
 
@@ -165,7 +165,7 @@ def load_train_test_data(train_dir, test_dir=None, image_filter=None, mask_filte
     # testing data
     test_images, test_labels, image_names_test = None, None, None
     if test_dir is not None:
-        image_names_test = get_image_files(test_dir, mask_filter, imf=image_filter)
+        image_names_test = get_image_files(test_dir, mask_filter, image_filter, look_one_level_down)
         label_names_test, flow_names_test = get_label_files(image_names_test, mask_filter, imf=image_filter)
         nimg = len(image_names_test)
         test_images = [imread(image_names_test[n]) for n in range(nimg)]

requirements.txt

@@ -0,0 +1,12 @@
+numpy~=1.19.3
+matplotlib~=3.3.2
+mxnet~=1.5.0
+natsort~=7.1.1
+scipy~=1.6.0
+pytest~=6.2.2
+tifffile~=2021.2.1
+pyqtgraph~=0.11.1
+tqdm~=4.56.0
+torch~=1.7.1
+numba~=0.52.0
+setuptools~=52.0.0