From a92a627c764f05c85bb01a9e60c337924b426c25 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 26 Sep 2019 15:10:25 +0200
Subject: [PATCH] Implement proper registration wrapper test and fix elastix
config parser issue
---
.../registration/apply_registration.py | 5 +-
test/registration/check_wrapper.py | 54 ---------
test/registration/test_wrapper.py | 107 ++++++++++++++++++
3 files changed, 109 insertions(+), 57 deletions(-)
delete mode 100644 test/registration/check_wrapper.py
create mode 100644 test/registration/test_wrapper.py
diff --git a/scripts/extension/registration/apply_registration.py b/scripts/extension/registration/apply_registration.py
index 8dd8b68..6116b75 100644
--- a/scripts/extension/registration/apply_registration.py
+++ b/scripts/extension/registration/apply_registration.py
@@ -56,7 +56,7 @@ class ApplyRegistrationBase(luigi.Task):
def update_line(line, to_write):
line = line.rstrip('\n')
line = line.split()
- line[1] = "\"%s\")" % to_write
+ line = [line[0], "\"%s\")" % to_write]
line = " ".join(line) + "\n"
return line
@@ -108,8 +108,7 @@ class ApplyRegistrationBase(luigi.Task):
assert self.interpolation in self.interpolation_modes
config = self.get_task_config()
- res_type = config.pop('res_type', None)
- # TODO what are valid res types?
+ res_type = config.pop('ResultImagePixelType', None)
if res_type is not None:
assert res_type in self.result_types
trafo_file = self.update_transformations(res_type)
diff --git a/test/registration/check_wrapper.py b/test/registration/check_wrapper.py
deleted file mode 100644
index 0f2eb02..0000000
--- a/test/registration/check_wrapper.py
+++ /dev/null
@@ -1,54 +0,0 @@
-import os
-import json
-
-import luigi
-from scripts.extension.registration import ApplyRegistrationLocal
-
-
-def check_wrapper():
- in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/ProSPr/stomach.tif'
-
- tmp_folder = os.path.abspath('tmp_registration')
- out_path = os.path.join(tmp_folder, 'stomach_prospr_registered')
-
- in_list = [in_path]
- out_list = [out_path]
- in_file = './in_list.json'
- with open(in_file, 'w') as f:
- json.dump(in_list, f)
- out_file = './out_list.json'
- with open(out_file, 'w') as f:
- json.dump(out_list, f)
-
- task = ApplyRegistrationLocal
- conf_dir = './configs'
- os.makedirs(conf_dir, exist_ok=True)
-
- global_conf = task.default_global_config()
- shebang = '/g/kreshuk/pape/Work/software/conda/miniconda3/envs/cluster_env37/bin/python'
- global_conf.update({'shebang': shebang})
- with open(os.path.join(conf_dir, 'global.config'), 'w') as f:
- json.dump(global_conf, f)
-
- trafo_dir = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/0.0.0/transformations'
-
- # This is the full transformation, but it takes a lot of time!
- trafo = os.path.join(trafo_dir, 'TransformParameters.BSpline10-3Channels.0.txt')
-
- # For now, we use the similarity trafo to save time
- trafo = os.path.join(trafo_dir, 'TransformParameters.Similarity-3Channels.0.txt')
-
- interpolation = 'nearest'
- t = task(tmp_folder=tmp_folder, config_dir=conf_dir, max_jobs=1,
- input_path_file=in_file, output_path_file=out_file, transformation_file=trafo,
- interpolation=interpolation)
- ret = luigi.build([t], local_scheduler=True)
- assert ret
- expected_xml = out_path + '.xml'
- assert os.path.exists(expected_xml), expected_xml
- expected_h5 = out_path + '.h5'
- assert os.path.exists(expected_h5), expected_h5
-
-
-if __name__ == '__main__':
- check_wrapper()
diff --git a/test/registration/test_wrapper.py b/test/registration/test_wrapper.py
new file mode 100644
index 0000000..3e958a5
--- /dev/null
+++ b/test/registration/test_wrapper.py
@@ -0,0 +1,107 @@
+import os
+import json
+import unittest
+
+import luigi
+import numpy as np
+import imageio
+from shutil import rmtree
+from scripts.extension.registration import ApplyRegistrationLocal
+
+
+class TestRegistrationWrapper(unittest.TestCase):
+ tmp_folder = './tmp_regestration'
+
+ def setUp(self):
+ os.makedirs(self.tmp_folder, exist_ok=True)
+
+ def tearDown(self):
+ try:
+ rmtree(self.tmp_folder)
+ except OSError:
+ pass
+
+ def _apply_registration(self, in_path, trafo_file, interpolation, file_format, dtype):
+ out_path = os.path.join(self.tmp_folder, 'out')
+
+ in_list = [in_path]
+ out_list = [out_path]
+ in_file = os.path.join(self.tmp_folder, 'in_list.json')
+ with open(in_file, 'w') as f:
+ json.dump(in_list, f)
+ out_file = os.path.join(self.tmp_folder, 'out_list.json')
+ with open(out_file, 'w') as f:
+ json.dump(out_list, f)
+
+ task = ApplyRegistrationLocal
+ conf_dir = os.path.join(self.tmp_folder, 'configs')
+ os.makedirs(conf_dir, exist_ok=True)
+
+ global_conf = task.default_global_config()
+ shebang = os.path.join('/g/arendt/EM_6dpf_segmentation/platy-browser-data/software/conda/miniconda3/envs',
+ 'platybrowser/bin/python')
+ global_conf.update({'shebang': shebang})
+ with open(os.path.join(conf_dir, 'global.config'), 'w') as f:
+ json.dump(global_conf, f)
+
+ task_conf = task.default_task_config()
+ task_conf.update({'threads_per_job': 8, 'ResultImagePixelType': dtype})
+ with open(os.path.join(conf_dir, 'apply_registration.config'), 'w') as f:
+ json.dump(task_conf, f)
+
+ t = task(tmp_folder=self.tmp_folder, config_dir=conf_dir, max_jobs=1,
+ input_path_file=in_file, output_path_file=out_file, transformation_file=trafo_file,
+ interpolation=interpolation, output_format=file_format)
+ ret = luigi.build([t], local_scheduler=True)
+ self.assertTrue(ret)
+ return out_path
+
+ # only makes sense for nearest neighbor interpolation
+ def check_result(self, in_path, res_path, check_range=False):
+ res = imageio.volread(res_path)
+ exp = imageio.volread(in_path).astype(res.dtype)
+
+ if check_range:
+ min_res = res.min()
+ min_exp = exp.min()
+ self.assertEqual(min_res, min_exp)
+ max_res = res.max()
+ max_exp = exp.max()
+ self.assertEqual(max_res, max_exp)
+ else:
+ un_res = np.unique(res)
+ un_exp = np.unique(exp)
+ self.assertTrue(np.array_equal(un_exp, un_res))
+
+ def test_nearest_mask(self):
+ trafo_dir = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/0.0.0/transformations'
+ # This is the full transformation, but it takes a lot of time!
+ # trafo_file = os.path.join(trafo_dir, 'TransformParameters.BSpline10-3Channels.0.txt')
+ # For now, we use the similarity trafo to save time
+ trafo_file = os.path.join(trafo_dir, 'TransformParameters.Similarity-3Channels.0.txt')
+
+ in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/ProSPr/stomach.tif'
+ out_path = self._apply_registration(in_path, trafo_file, 'nearest', 'tif', 'unsigned char')
+
+ out_path = out_path + '-ch0.tif'
+ self.assertTrue(os.path.exists(out_path))
+ self.check_result(in_path, out_path)
+
+ def test_nearest_seg(self):
+ trafo_dir = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/0.0.0/transformations'
+ # This is the full transformation, but it takes a lot of time!
+ # trafo_file = os.path.join(trafo_dir, 'TransformParameters.BSpline10-3Channels.0.txt')
+ # For now, we use the similarity trafo to save time
+ trafo_file = os.path.join(trafo_dir, 'TransformParameters.Similarity-3Channels.0.txt')
+
+ in_path = '/g/kreshuk/zinchenk/cell_match/data/genes/vc_volume_prospr_space_all_vc.tif'
+ out_path = self._apply_registration(in_path, trafo_file, 'nearest', 'tif', 'unsigned short')
+
+ out_path = out_path + '-ch0.tif'
+ self.assertTrue(os.path.exists(out_path))
+ # we can only check the range for segmentations, because individual ids might be lost
+ self.check_result(in_path, out_path, check_range=True)
+
+
+if __name__ == '__main__':
+ unittest.main()
--
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