From 0af98c8ad71ba584cdc3e57ed3d51d9f9cf7f056 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Fri, 20 Sep 2019 15:29:50 +0200
Subject: [PATCH] Debugging apply_registration WIP
---
.../registration/apply_registration.py | 17 ++++++++++++++---
test/registration/check_wrapper.py | 3 ++-
2 files changed, 16 insertions(+), 4 deletions(-)
diff --git a/scripts/extension/registration/apply_registration.py b/scripts/extension/registration/apply_registration.py
index 01631ae..41f6ab6 100644
--- a/scripts/extension/registration/apply_registration.py
+++ b/scripts/extension/registration/apply_registration.py
@@ -123,15 +123,26 @@ def apply_for_file(input_path, output_path,
# "elastixDirectory='/g/almf/software/elastix_v4.8', workingDirectory='$TMPDIR',
# inputImageFile='$INPUT_IMAGE',transformationFile='/g/cba/exchange/platy-trafos/linear/TransformParameters.BSpline10-3Channels.0.txt
# outputFile='$OUTPUT_IMAGE',outputModality='Save as BigDataViewer .xml/.h5',numThreads='1'"
- # NOTE: I ommit --run here, because fiji throws a warning that it does not recognise the argument
- cmd = [fiji_executable, "--ij2", "--headless", "\"Transformix\"", transformix_argument]
+ cmd = [fiji_executable, "--ij2", "--headless", "--run", "\"Transformix\"", transformix_argument]
cmd_str = " ".join(cmd)
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
+
try:
- check_output(cmd)
+ # check_output(cmd)
+ # the CLI parser is very awkward (to put it nicely).
+ # 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
+ # throwing a warning:
+ # [WARNING] Ignoring invalid argument: --run
+ check_output([cmd_str], shell=True)
except CalledProcessError as e:
raise RuntimeError(e.output)
diff --git a/test/registration/check_wrapper.py b/test/registration/check_wrapper.py
index 12fa5bc..6313f72 100644
--- a/test/registration/check_wrapper.py
+++ b/test/registration/check_wrapper.py
@@ -9,7 +9,8 @@ from scripts.extension.registration import ApplyRegistrationLocal
def check_wrapper():
- in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/images/ProSPr/Stomach_forRegistration.tif'
+ 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]
--
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