Fix imagej

.github/workflows/tests.yml

@@ -28,10 +28,12 @@ jobs:
       run: python -c "import sys; print(sys.version)"
     - name: Install dependencies
       run: |
+        sudo apt-get update
+        sudo apt-get install -qq libtiff5-dev
         python -m pip install --upgrade pip
         pip install flake8 pytest coverage
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install scikit-image libtiff
+        pip install scikit-image
     - name: Test with pytest
       run: |
         coverage run --source=concert -m pytest -m "not skip_ci"

concert/ext/viewers.py

@@ -2,12 +2,9 @@
 import asyncio
 import collections
 import multiprocessing as mp
-import os
-import tempfile
 import time
 import logging
 from queue import Empty
-from subprocess import Popen
 from typing import Callable
 import numpy as np
 from concert.base import Parameterizable, Parameter
@@ -19,31 +16,34 @@
 _MP_CTX = mp.get_context('spawn')
 
 
+def _start_command(program, image):
+    """
+    Create a tmp file for dumping the *image* and use *program*
+    to open that image. Use *writer* for writing the iamge to the disk.
+    """
+    import os
+    import tempfile
+    from subprocess import Popen
+    from concert.storage import write_tiff
+
+    tmp_file = tempfile.mkstemp()[1]
+    try:
+        full_path = write_tiff(tmp_file, image)
+        with Popen([program, full_path]) as process:
+            process.wait()
+    finally:
+        os.remove(full_path)
+
+
 def imagej(image, path="imagej"):
     """
     imagej(image, path="imagej")
 
     Open *image* in ImageJ found by *path*.
     """
-    def start_command(program, image):
-        """
-        Create a tmp file for dumping the *image* and use *program*
-        to open that image. Use *writer* for writing the iamge to the disk.
-        """
-        from concert.storage import write_tiff
-
-        tmp_file = tempfile.mkstemp()[1]
-        try:
-            full_path = write_tiff(tmp_file, image)
-            with Popen([program, full_path]) as process:
-                process.wait()
-        finally:
-            os.remove(full_path)
-            LOG.debug('Temporary file removed')
-
     # Do not make a daemon process to make sure the interpreter waits for it to exit, i.e. the
     # *finally* will be called and temp file deleted.
-    proc = _MP_CTX.Process(target=start_command, args=(path, image), daemon=False)
+    proc = _MP_CTX.Process(target=_start_command, args=(path, image), daemon=False)
     proc.start()
 
 

concert/tests/integration/test_ext.py

@@ -0,0 +1,15 @@
+import multiprocessing as mp
+import numpy as np
+from concert.ext.viewers import _start_command
+from concert.tests import suppressed_logging
+
+
+_MP_CTX = mp.get_context('spawn')
+
+
+@suppressed_logging
+def test_start_command():
+    image = np.arange(25).reshape(5, 5).astype(np.float32)
+    proc = _MP_CTX.Process(target=_start_command, args=("echo", image), daemon=False)
+    proc.start()
+    proc.join()