fixing loading from txt file with dask (#24)

* fixing loading from txt file
hotfix for brainglobe/cellfinder#184

* added unittests for IO

* fixed side effect with tests searching for subdirectories
moved brain_paths.txt to brain directory
replaced paths with constants

cellfinder_core/tools/IO.py

@@ -33,7 +33,12 @@ def read_with_dask(path):
     :return:
     """
 
-    filenames = glob.glob(os.path.join(path, "*.tif"))
+    if path.endswith(".txt"):
+        with open(path, "r") as f:
+            filenames = [line.rstrip() for line in f.readlines()]
+
+    else:
+        filenames = glob.glob(os.path.join(path, "*.tif"))
 
     shape, dtype = get_tiff_meta(filenames[0])
     lazy_arrays = [lazy_imread(fn) for fn in get_sorted_file_paths(filenames)]

tests/data/brain/brain_paths.txt

@@ -0,0 +1,270 @@
+tests/data/brain/image_0000.tif
+tests/data/brain/image_0001.tif
+tests/data/brain/image_0002.tif
+tests/data/brain/image_0003.tif
+tests/data/brain/image_0004.tif
+tests/data/brain/image_0005.tif
+tests/data/brain/image_0006.tif
+tests/data/brain/image_0007.tif
+tests/data/brain/image_0008.tif
+tests/data/brain/image_0009.tif
+tests/data/brain/image_0010.tif
+tests/data/brain/image_0011.tif
+tests/data/brain/image_0012.tif
+tests/data/brain/image_0013.tif
+tests/data/brain/image_0014.tif
+tests/data/brain/image_0015.tif
+tests/data/brain/image_0016.tif
+tests/data/brain/image_0017.tif
+tests/data/brain/image_0018.tif
+tests/data/brain/image_0019.tif
+tests/data/brain/image_0020.tif
+tests/data/brain/image_0021.tif
+tests/data/brain/image_0022.tif
+tests/data/brain/image_0023.tif
+tests/data/brain/image_0024.tif
+tests/data/brain/image_0025.tif
+tests/data/brain/image_0026.tif
+tests/data/brain/image_0027.tif
+tests/data/brain/image_0028.tif
+tests/data/brain/image_0029.tif
+tests/data/brain/image_0030.tif
+tests/data/brain/image_0031.tif
+tests/data/brain/image_0032.tif
+tests/data/brain/image_0033.tif
+tests/data/brain/image_0034.tif
+tests/data/brain/image_0035.tif
+tests/data/brain/image_0036.tif
+tests/data/brain/image_0037.tif
+tests/data/brain/image_0038.tif
+tests/data/brain/image_0039.tif
+tests/data/brain/image_0040.tif
+tests/data/brain/image_0041.tif
+tests/data/brain/image_0042.tif
+tests/data/brain/image_0043.tif
+tests/data/brain/image_0044.tif
+tests/data/brain/image_0045.tif
+tests/data/brain/image_0046.tif
+tests/data/brain/image_0047.tif
+tests/data/brain/image_0048.tif
+tests/data/brain/image_0049.tif
+tests/data/brain/image_0050.tif
+tests/data/brain/image_0051.tif
+tests/data/brain/image_0052.tif
+tests/data/brain/image_0053.tif
+tests/data/brain/image_0054.tif
+tests/data/brain/image_0055.tif
+tests/data/brain/image_0056.tif
+tests/data/brain/image_0057.tif
+tests/data/brain/image_0058.tif
+tests/data/brain/image_0059.tif
+tests/data/brain/image_0060.tif
+tests/data/brain/image_0061.tif
+tests/data/brain/image_0062.tif
+tests/data/brain/image_0063.tif
+tests/data/brain/image_0064.tif
+tests/data/brain/image_0065.tif
+tests/data/brain/image_0066.tif
+tests/data/brain/image_0067.tif
+tests/data/brain/image_0068.tif
+tests/data/brain/image_0069.tif
+tests/data/brain/image_0070.tif
+tests/data/brain/image_0071.tif
+tests/data/brain/image_0072.tif
+tests/data/brain/image_0073.tif
+tests/data/brain/image_0074.tif
+tests/data/brain/image_0075.tif
+tests/data/brain/image_0076.tif
+tests/data/brain/image_0077.tif
+tests/data/brain/image_0078.tif
+tests/data/brain/image_0079.tif
+tests/data/brain/image_0080.tif
+tests/data/brain/image_0081.tif
+tests/data/brain/image_0082.tif
+tests/data/brain/image_0083.tif
+tests/data/brain/image_0084.tif
+tests/data/brain/image_0085.tif
+tests/data/brain/image_0086.tif
+tests/data/brain/image_0087.tif
+tests/data/brain/image_0088.tif
+tests/data/brain/image_0089.tif
+tests/data/brain/image_0090.tif
+tests/data/brain/image_0091.tif
+tests/data/brain/image_0092.tif
+tests/data/brain/image_0093.tif
+tests/data/brain/image_0094.tif
+tests/data/brain/image_0095.tif
+tests/data/brain/image_0096.tif
+tests/data/brain/image_0097.tif
+tests/data/brain/image_0098.tif
+tests/data/brain/image_0099.tif
+tests/data/brain/image_0100.tif
+tests/data/brain/image_0101.tif
+tests/data/brain/image_0102.tif
+tests/data/brain/image_0103.tif
+tests/data/brain/image_0104.tif
+tests/data/brain/image_0105.tif
+tests/data/brain/image_0106.tif
+tests/data/brain/image_0107.tif
+tests/data/brain/image_0108.tif
+tests/data/brain/image_0109.tif
+tests/data/brain/image_0110.tif
+tests/data/brain/image_0111.tif
+tests/data/brain/image_0112.tif
+tests/data/brain/image_0113.tif
+tests/data/brain/image_0114.tif
+tests/data/brain/image_0115.tif
+tests/data/brain/image_0116.tif
+tests/data/brain/image_0117.tif
+tests/data/brain/image_0118.tif
+tests/data/brain/image_0119.tif
+tests/data/brain/image_0120.tif
+tests/data/brain/image_0121.tif
+tests/data/brain/image_0122.tif
+tests/data/brain/image_0123.tif
+tests/data/brain/image_0124.tif
+tests/data/brain/image_0125.tif
+tests/data/brain/image_0126.tif
+tests/data/brain/image_0127.tif
+tests/data/brain/image_0128.tif
+tests/data/brain/image_0129.tif
+tests/data/brain/image_0130.tif
+tests/data/brain/image_0131.tif
+tests/data/brain/image_0132.tif
+tests/data/brain/image_0133.tif
+tests/data/brain/image_0134.tif
+tests/data/brain/image_0135.tif
+tests/data/brain/image_0136.tif
+tests/data/brain/image_0137.tif
+tests/data/brain/image_0138.tif
+tests/data/brain/image_0139.tif
+tests/data/brain/image_0140.tif
+tests/data/brain/image_0141.tif
+tests/data/brain/image_0142.tif
+tests/data/brain/image_0143.tif
+tests/data/brain/image_0144.tif
+tests/data/brain/image_0145.tif
+tests/data/brain/image_0146.tif
+tests/data/brain/image_0147.tif
+tests/data/brain/image_0148.tif
+tests/data/brain/image_0149.tif
+tests/data/brain/image_0150.tif
+tests/data/brain/image_0151.tif
+tests/data/brain/image_0152.tif
+tests/data/brain/image_0153.tif
+tests/data/brain/image_0154.tif
+tests/data/brain/image_0155.tif
+tests/data/brain/image_0156.tif
+tests/data/brain/image_0157.tif
+tests/data/brain/image_0158.tif
+tests/data/brain/image_0159.tif
+tests/data/brain/image_0160.tif
+tests/data/brain/image_0161.tif
+tests/data/brain/image_0162.tif
+tests/data/brain/image_0163.tif
+tests/data/brain/image_0164.tif
+tests/data/brain/image_0165.tif
+tests/data/brain/image_0166.tif
+tests/data/brain/image_0167.tif
+tests/data/brain/image_0168.tif
+tests/data/brain/image_0169.tif
+tests/data/brain/image_0170.tif
+tests/data/brain/image_0171.tif
+tests/data/brain/image_0172.tif
+tests/data/brain/image_0173.tif
+tests/data/brain/image_0174.tif
+tests/data/brain/image_0175.tif
+tests/data/brain/image_0176.tif
+tests/data/brain/image_0177.tif
+tests/data/brain/image_0178.tif
+tests/data/brain/image_0179.tif
+tests/data/brain/image_0180.tif
+tests/data/brain/image_0181.tif
+tests/data/brain/image_0182.tif
+tests/data/brain/image_0183.tif
+tests/data/brain/image_0184.tif
+tests/data/brain/image_0185.tif
+tests/data/brain/image_0186.tif
+tests/data/brain/image_0187.tif
+tests/data/brain/image_0188.tif
+tests/data/brain/image_0189.tif
+tests/data/brain/image_0190.tif
+tests/data/brain/image_0191.tif
+tests/data/brain/image_0192.tif
+tests/data/brain/image_0193.tif
+tests/data/brain/image_0194.tif
+tests/data/brain/image_0195.tif
+tests/data/brain/image_0196.tif
+tests/data/brain/image_0197.tif
+tests/data/brain/image_0198.tif
+tests/data/brain/image_0199.tif
+tests/data/brain/image_0200.tif
+tests/data/brain/image_0201.tif
+tests/data/brain/image_0202.tif
+tests/data/brain/image_0203.tif
+tests/data/brain/image_0204.tif
+tests/data/brain/image_0205.tif
+tests/data/brain/image_0206.tif
+tests/data/brain/image_0207.tif
+tests/data/brain/image_0208.tif
+tests/data/brain/image_0209.tif
+tests/data/brain/image_0210.tif
+tests/data/brain/image_0211.tif
+tests/data/brain/image_0212.tif
+tests/data/brain/image_0213.tif
+tests/data/brain/image_0214.tif
+tests/data/brain/image_0215.tif
+tests/data/brain/image_0216.tif
+tests/data/brain/image_0217.tif
+tests/data/brain/image_0218.tif
+tests/data/brain/image_0219.tif
+tests/data/brain/image_0220.tif
+tests/data/brain/image_0221.tif
+tests/data/brain/image_0222.tif
+tests/data/brain/image_0223.tif
+tests/data/brain/image_0224.tif
+tests/data/brain/image_0225.tif
+tests/data/brain/image_0226.tif
+tests/data/brain/image_0227.tif
+tests/data/brain/image_0228.tif
+tests/data/brain/image_0229.tif
+tests/data/brain/image_0230.tif
+tests/data/brain/image_0231.tif
+tests/data/brain/image_0232.tif
+tests/data/brain/image_0233.tif
+tests/data/brain/image_0234.tif
+tests/data/brain/image_0235.tif
+tests/data/brain/image_0236.tif
+tests/data/brain/image_0237.tif
+tests/data/brain/image_0238.tif
+tests/data/brain/image_0239.tif
+tests/data/brain/image_0240.tif
+tests/data/brain/image_0241.tif
+tests/data/brain/image_0242.tif
+tests/data/brain/image_0243.tif
+tests/data/brain/image_0244.tif
+tests/data/brain/image_0245.tif
+tests/data/brain/image_0246.tif
+tests/data/brain/image_0247.tif
+tests/data/brain/image_0248.tif
+tests/data/brain/image_0249.tif
+tests/data/brain/image_0250.tif
+tests/data/brain/image_0251.tif
+tests/data/brain/image_0252.tif
+tests/data/brain/image_0253.tif
+tests/data/brain/image_0254.tif
+tests/data/brain/image_0255.tif
+tests/data/brain/image_0256.tif
+tests/data/brain/image_0257.tif
+tests/data/brain/image_0258.tif
+tests/data/brain/image_0259.tif
+tests/data/brain/image_0260.tif
+tests/data/brain/image_0261.tif
+tests/data/brain/image_0262.tif
+tests/data/brain/image_0263.tif
+tests/data/brain/image_0264.tif
+tests/data/brain/image_0265.tif
+tests/data/brain/image_0266.tif
+tests/data/brain/image_0267.tif
+tests/data/brain/image_0268.tif
+tests/data/brain/image_0269.tif

tests/tests/test_unit/test_tools/test_IO.py

@@ -0,0 +1,18 @@
+import dask.array as d_array
+
+from cellfinder_core.tools import IO
+
+BRAIN_DIR = "tests/data/brain"
+BRAIN_PATHS = f"{BRAIN_DIR}/brain_paths.txt"
+
+
+def test_read_with_dask_txt():
+    stack = IO.read_with_dask(BRAIN_PATHS)
+    assert type(stack) == d_array.Array
+
+
+def test_read_with_dask_glob_txt_equal():
+    txt_stack = IO.read_with_dask(BRAIN_PATHS)
+    glob_stack = IO.read_with_dask(BRAIN_DIR)
+
+    assert d_array.equal(txt_stack, glob_stack).all()