From e8bec9d1b4fb13e5636b03decd46aa89124ac5a2 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Mon, 23 Sep 2019 11:00:59 +0200
Subject: [PATCH] Update apply_registration
---
.../registration/apply_registration.py | 29 +++++----
test/registration/check_wrapper.py | 63 +++++--------------
2 files changed, 34 insertions(+), 58 deletions(-)
diff --git a/scripts/extension/registration/apply_registration.py b/scripts/extension/registration/apply_registration.py
index 41f6ab6..7fa913a 100644
--- a/scripts/extension/registration/apply_registration.py
+++ b/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):
diff --git a/test/registration/check_wrapper.py b/test/registration/check_wrapper.py
index 5052cfe..5a381c3 100644
--- a/test/registration/check_wrapper.py
+++ b/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()
--
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