Update apply_registration

scripts/extension/registration/apply_registration.py

@@ -15,6 +15,8 @@ from cluster_tools.cluster_tasks import SlurmTask, LocalTask, LSFTask
 class ApplyRegistrationBase(luigi.Task):
     """ ApplyRegistration base class
     """
+    default_fiji = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/software/Fiji.app/ImageJ-linux64'
+    default_elastix = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/software/elastix_v4.8'
 
     task_name = 'apply_registration'
     src_file = os.path.abspath(__file__)
@@ -23,8 +25,8 @@ class ApplyRegistrationBase(luigi.Task):
     input_path_file = luigi.Parameter()
     output_path_file = luigi.Parameter()
     transformation_file = luigi.Parameter()
-    fiji_executable = luigi.Parameter(default='/g/almf/software/Fiji.app/ImageJ-linux64')
-    elastix_directory = luigi.Parameter(default='/g/almf/software/elastix_v4.8')
+    fiji_executable = luigi.Parameter(default=default_fiji)
+    elastix_directory = luigi.Parameter(default=default_elastix)
     dependency = luigi.TaskParameter(default=DummyTask())
 
     def requires(self):
@@ -108,12 +110,12 @@ def apply_for_file(input_path, output_path,
     # with individual arguments comma separated
     # the argument to transformaix needs to be one large comma separated string
     transformix_argument = ["elastixDirectory=\'%s\'" % elastix_directory,
-                            "workingDirectory=\'%s\'" % tmp_folder,
+                            "workingDirectory=\'%s\'" % os.path.abspath(tmp_folder),
                             "inputImageFile=\'%s\'" % input_path,
                             "transformationFile=\'%s\'" % transformation_file,
                             "outputFile=\'%s\'" % output_path,
                             "outputModality=\'Save as BigDataViewer .xml/.h5\'",
-                            "numThreads=\'1\'"]  # TODO why do we use numThreads=1 and not the same as in -c?
+                            "numThreads=\'%i\'" % n_threads]
     transformix_argument = ",".join(transformix_argument)
     transformix_argument = "\"%s\"" % transformix_argument
 
@@ -129,14 +131,16 @@ def apply_for_file(input_path, output_path,
     fu.log("Calling the following command:")
     fu.log(cmd_str)
 
-    # the elastix wrapper only works properly if we set these as environment variables as well, see
-    # TODO make issue about this
-    # os.environ['TMPDIR'] = tmp_folder
-    os.environ['TRAFO'] = transformation_file
-
+    cwd = os.getcwd()
     try:
+        # we need to change the working dir to the transformation directroy, so that relative paths in
+        # the transformations are correct
+        trafo_dir = os.path.split(transformation_file)[0]
+        fu.log("Change directory to %s" % trafo_dir)
+        os.chdir(trafo_dir)
+
         # check_output(cmd)
-        # the CLI parser is very awkward (to put it nicely).
+        # the CLI parser is very awkward.
         # I could only get it to work by passing the whole command string
         # and setting shell to True.
         # otherwise, it would parse something wrong, and do nothing but
@@ -144,7 +148,10 @@ def apply_for_file(input_path, output_path,
         # [WARNING] Ignoring invalid argument: --run
         check_output([cmd_str], shell=True)
     except CalledProcessError as e:
-        raise RuntimeError(e.output)
+        raise RuntimeError(e.output.decode('utf-8'))
+    finally:
+        fu.log("Go back to cwd: %s" % cwd)
+        os.chdir(cwd)
 
 
 def apply_registration(job_id, config_path):

test/registration/check_wrapper.py

@@ -2,17 +2,14 @@ import os
 import json
 
 import luigi
-# TODO remove path hack once we merge this into master
-import sys
-sys.path.insert(0, '../..')
 from scripts.extension.registration import ApplyRegistrationLocal
 
 
-def check_wrapper_simple():
-    in_path = '/g/almf/software/elastix-test/muscles.tif'
+def check_wrapper():
+    in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/ProSPr/stomach.tif'
 
-    tmp_folder = '/g/kreshuk/pape/Work/my_projects/dev-platy/test/registration/tmp_registration_simple'
-    out_path = os.path.join(tmp_folder, 'out')
+    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]
@@ -33,51 +30,23 @@ def check_wrapper_simple():
     with open(os.path.join(conf_dir, 'global.config'), 'w') as f:
         json.dump(global_conf, f)
 
-    trafo = '/g/almf/software/elastix-test/TransformParameters.RotationPreAlign.0.txt'
-    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)
-    ret = luigi.build([t], local_scheduler=True)
-    assert ret
-    expected_out_xml = out_path + '.xml'
-    assert os.path.exists(expected_out_xml), expected_out_xml
-    expected_out_h5 = out_path + '.h5'
-    assert os.path.exists(expected_out_h5), expected_out_h5
-
-
-def check_wrapper():
-    in_path = os.path.join('/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/images/ProSPr',
-                           'Stomach_forRegistration.tif')
-    out_path = '/g/kreshuk/pape/Work/my_projects/dev-platy/test/registration/somach_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)
+    trafo_dir = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/0.0.0/transformations'
 
-    task = ApplyRegistrationLocal
-    conf_dir = './configs'
-    os.makedirs(conf_dir, exist_ok=True)
+    # This is the full transformation, but it takes a lot of time!
+    trafo = os.path.join(trafo_dir, 'TransformParameters.BSpline10-3Channels.0.txt')
 
-    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)
+    # For now, we use the similarity trafo to save time
+    trafo = os.path.join(trafo_dir, 'TransformParameters.Similarity-3Channels.0.txt')
 
-    # TODO which one is the correct trafo ?
-    trafo = os.path.join('/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/0.0.0/transformations/0.0.0',
-                         'TransformParameters.BSpline10-3Channels.0.txt')
-    t = task(tmp_folder='tmp_registration', config_dir=conf_dir, max_jobs=1,
+    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)
     ret = luigi.build([t], local_scheduler=True)
     assert ret
-    expected_out = out_path + '.xml'
-    assert os.path.exists(expected_out), expected_out
+    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
 
 
-# check_wrapper()
-check_wrapper_simple()
+if __name__ == '__main__':
+    check_wrapper()