Add flat files to test data

Neural-Systems-at-UIO · Nov 7, 2024 · 446b1df · 446b1df
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commit 446b1df
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Showing 17 changed files with 8 additions and 1 deletion.
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/report.tsv b/tests/test_data/nonlinear_allen_mouse/flat_files/report.tsv
@@ -0,0 +1,6 @@
+snr	name	segmented	changed	stable%
+1	test_s001.png	64578	2991	95%
+2	test_s002.png	83702	34124	59%
+3	test_s003.png	93593	67152	28%
+4	test_s004.png	97022	44431	54%
+5	test_s005.png	92810	90411	2%
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.flat
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl_rbw.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.flat
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl_rbw.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl.flat
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s003_nl_rbw.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.flat
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl_rbw.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl.flat
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl.png
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl_rbw.png
diff --git a/workflows/basic_example_custom_atlas.py b/workflows/basic_example_custom_atlas.py
@@ -12,6 +12,7 @@
 ###The atlas_path is the path to the relevant atlas.nrrd
 ###The label_path is the path to the corresponding atlas .csv
 ###The object_cutoff is a cut-off for min object size
+### get_coordinates, if use_flat=True, place flat files in folder titled "flat_files" at same level as "segmentations" folder 
 
 pnt = PyNutil(
     segmentation_folder="../tests/test_data/linear_allen_mouse/",
@@ -20,6 +21,6 @@
     atlas_path="../tests/test_data/allen_mouse_2017_atlas/annotation_25_reoriented_2017.nrrd",
     label_path="../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv",
 )
-pnt.get_coordinates(object_cutoff=0)
+pnt.get_coordinates(object_cutoff=0, use_flat=True)
 pnt.quantify_coordinates()
 pnt.save_analysis("../test_result/test_linear_allen_mouse")