Add test for region attributes

test/attributes/test_regions.py

+import unittest
+import sys
+import os
+import json
+from shutil import rmtree
+
+import numpy as np
+import pandas
+import h5py
+from cluster_tools.node_labels import NodeLabelWorkflow
+sys.path.append('../..')
+
+
+# check new version of gene mapping against original
+class TestRegions(unittest.TestCase):
+    tmp_folder = 'tmp'
+
+    def tearDown(self):
+        try:
+            rmtree(self.tmp_folder)
+        except OSError:
+            pass
+
+    def check_result(self, table, base_table,
+                     seg_path, seg_key,
+                     tissue_path, tissue_key):
+
+        resolution = [.1, .08, .08]
+
+        with h5py.File(seg_path, 'r') as fseg, h5py.File(tissue_path, 'r') as ftis:
+            ds_seg = fseg[seg_key]
+            ds_tis = ftis[tissue_key]
+            assert ds_seg.shape == ds_tis.shape, "%s, %s" % (str(ds_seg.shape),
+                                                             str(ds_tis.shape))
+
+            names = ftis['semantic_names'][:]
+            mapped_ids = ftis['semantic_mapping'][:]
+
+            for name, tis_ids in zip(names, mapped_ids):
+
+                # these are too big
+                if name in ('cuticle', 'neuropil'):
+                    continue
+                print("Checking", name)
+
+                col = table[name].values
+                seg_ids = np.where(col == 1.)[0]
+                for seg_id in seg_ids:
+                    row = base_table.iloc[seg_id]
+                    bb_start = [row.bb_min_z, row.bb_min_y, row.bb_min_x]
+                    bb_stop = [row.bb_max_z, row.bb_max_y, row.bb_max_x]
+                    bb = tuple(slice(int(mi / re), int(ma / re))
+                               for mi, ma, re in zip(bb_start, bb_stop, resolution))
+
+                    seg = ds_seg[bb]
+                    tis = ds_tis[bb]
+
+                    seg_mask = seg == seg_id
+                    self.assertGreater(np.in1d(tis[seg_mask], tis_ids).sum(), 0)
+
+    def test_regions(self):
+        from scripts.attributes.region_attributes import region_attributes
+
+        segmentation_folder = '../../data/0.0.0/segmentations'
+        seg_path = os.path.join(segmentation_folder,
+                                'sbem-6dpf-1-whole-segmented-cells-labels.h5')
+        seg_key = 't00000/s00/0/cells'
+        with h5py.File(seg_path, 'r') as f:
+            max_id = f[seg_key].attrs['maxId']
+
+        output_path = os.path.join(self.tmp_folder, 'table-test.csv')
+        label_ids = np.arange(max_id + 1, dtype='uint64')
+
+        # write the global config
+        config_folder = os.path.join(self.tmp_folder, 'configs')
+        os.makedirs(config_folder, exist_ok=True)
+        conf = NodeLabelWorkflow.get_config()['global']
+        shebang = '#! /g/kreshuk/pape/Work/software/conda/miniconda3/envs/cluster_env37/bin/python'
+        conf.update({'shebang': shebang})
+        with open(os.path.join(config_folder, 'global.config'), 'w') as f:
+            json.dump(conf, f)
+
+        target = 'local'
+        max_jobs = 32
+        region_attributes(seg_path, output_path, segmentation_folder,
+                          label_ids, self.tmp_folder, target, max_jobs)
+
+        table = pandas.read_csv(output_path, sep='\t')
+        assert len(table) == max_id + 1
+
+        base_path = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv'
+        base_table = pandas.read_csv(base_path, sep='\t')
+
+        seg_key = 't00000/s00/2/cells'
+        tissue_path = '../../data/rawdata/sbem-6dpf-1-whole-segmented-tissue-labels.h5'
+        tissue_key = 't00000/s00/0/cells'
+        self.check_result(table, base_table,
+                          seg_path, seg_key,
+                          tissue_path, tissue_key)
+
+
+# this indeed fails for the glands, whereas the unittest above passes
+def check_external():
+    t = TestRegions()
+
+    base_table_path = '/g/arendt/EM_6dpf_segmentation/EM-Prospr/tables/em-segmented-cells-20190520-labels.csv'
+    base_table = pandas.read_csv(base_table_path, sep='\t')
+
+    table_path = '/g/kreshuk/pape/Work/my_projects/py_platy_browser/experiments/segmentation/tissue/regions.csv'
+    table = pandas.read_csv(table_path, sep='\t')
+
+    seg_path = '/g/arendt/EM_6dpf_segmentation/EM-Prospr/em-segmented-cells-20190520-labels.h5'
+    tissue_path = '/g/arendt/EM_6dpf_segmentation/EM-Prospr/em-segmented-tissue-labels.h5'
+    seg_key = 't00000/s00/2/cells'
+    tissue_key = 't00000/s00/0/cells'
+
+    t.check_result(table, base_table,
+                   seg_path, seg_key,
+                   tissue_path, tissue_key)
+
+
+if __name__ == '__main__':
+    # check_external()
+    unittest.main()