junifer 0.0.4.dev422__tar.gz → 0.0.4.dev428__tar.gz

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev422
+Version: 0.0.4.dev428
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.4.dev428/docs/changes/newsfragments/278.bugfix

@@ -0,0 +1 @@
+Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_

junifer-0.0.4.dev428/docs/changes/newsfragments/279.misc

@@ -0,0 +1 @@
+Make the external tool wrappers output to stderr instead of stdout by `Synchon Mandal`_

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev422'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev422')
+__version__ = version = '0.0.4.dev428'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev428')

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer/api/res/afni/run_afni_docker.sh

@@ -6,7 +6,7 @@ mounts=0
 for var in "$@"
 do
 if [ -d "${var}" ]; then
-        echo "$var is a directory"
+        echo "$var is a directory" >&2
         var=$(realpath "${var}")
         host_dir=$(dirname "${var}")
         ((mounts+=1))
@@ -15,10 +15,10 @@ if [ -d "${var}" ]; then
         var=${container_dir}
     elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
         if [ -f "${var}" ]; then
-            echo "$var is a file"
+            echo "$var is a file" >&2
             var=$(realpath "${var}")
         else
-            echo "$var is a prefix"
+            echo "$var is a prefix" >&2
         fi
         fname=$(basename "${var}")
         host_dir=$(dirname "${var}")
@@ -30,10 +30,10 @@ if [ -d "${var}" ]; then
     corrected_args+=("${var}")
 done
 
-echo "Docker args: ${docker_args[*]}"
-echo "Corrected args for afni: ${corrected_args[*]}"
+echo "Docker args: ${docker_args[*]}" >&2
+echo "Corrected args for afni: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"
-echo "Running command: ${cmd}"
+echo "Running command: ${cmd}" >&2
 ${cmd}

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer/api/res/ants/run_ants_docker.sh

@@ -6,7 +6,7 @@ mounts=0
 for var in "$@"
 do
 if [ -d "${var}" ]; then
-        echo "$var is a directory"
+        echo "$var is a directory" >&2
         var=$(realpath "${var}")
         host_dir=$(dirname "${var}")
         ((mounts+=1))
@@ -15,10 +15,10 @@ if [ -d "${var}" ]; then
         var=${container_dir}
     elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
         if [ -f "${var}" ]; then
-            echo "$var is a file"
+            echo "$var is a file" >&2
             var=$(realpath "${var}")
         else
-            echo "$var is a prefix"
+            echo "$var is a prefix" >&2
         fi
         fname=$(basename "${var}")
         host_dir=$(dirname "${var}")
@@ -30,10 +30,10 @@ if [ -d "${var}" ]; then
     corrected_args+=("${var}")
 done
 
-echo "Docker args: ${docker_args[*]}"
-echo "Corrected args for fsl: ${corrected_args[*]}"
+echo "Docker args: ${docker_args[*]}" >&2
+echo "Corrected args for fsl: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"
-echo "Running command: ${cmd}"
+echo "Running command: ${cmd}" >&2
 ${cmd}

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer/api/res/fsl/run_fsl_docker.sh

@@ -6,7 +6,7 @@ mounts=0
 for var in "$@"
 do
 if [ -d "${var}" ]; then
-        echo "$var is a directory"
+        echo "$var is a directory" >&2
         var=$(realpath "${var}")
         host_dir=$(dirname "${var}")
         ((mounts+=1))
@@ -15,10 +15,10 @@ if [ -d "${var}" ]; then
         var=${container_dir}
     elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
         if [ -f "${var}" ]; then
-            echo "$var is a file"
+            echo "$var is a file" >&2
             var=$(realpath "${var}")
         else
-            echo "$var is a prefix"
+            echo "$var is a prefix" >&2
         fi
         fname=$(basename "${var}")
         host_dir=$(dirname "${var}")
@@ -30,10 +30,10 @@ if [ -d "${var}" ]; then
     corrected_args+=("${var}")
 done
 
-echo "Docker args: ${docker_args[*]}"
-echo "Corrected args for fsl: ${corrected_args[*]}"
+echo "Docker args: ${docker_args[*]}" >&2
+echo "Corrected args for fsl: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"
-echo "Running command: ${cmd}"
+echo "Running command: ${cmd}" >&2
 ${cmd}

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer/data/coordinates.py

@@ -260,11 +260,12 @@ def get_coordinates(
         std2imgcoord_out_path = element_tempdir / "coordinates_transformed.txt"
         # Set std2imgcoord command
         std2imgcoord_cmd = [
-            "std2imgcoord",
+            "cat",
+            f"{pretransform_coordinates_path.resolve()}",
+            "| std2imgcoord",
             f"-img {target_data['reference_path'].resolve()}",
             f"-warp {extra_input['Warp']['path'].resolve()}",
-            f"{pretransform_coordinates_path.resolve()}",
-            f"> {std2imgcoord_out_path.resolve()}",
+            f"- > {std2imgcoord_out_path.resolve()}",
         ]
         # Call std2imgcoord
         std2imgcoord_cmd_str = " ".join(std2imgcoord_cmd)

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev422
+Version: 0.0.4.dev428
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.4.dev422 → junifer-0.0.4.dev428}/junifer.egg-info/SOURCES.txt

@@ -87,6 +87,8 @@ docs/changes/newsfragments/272.bugfix
 docs/changes/newsfragments/274.bugfix
 docs/changes/newsfragments/276.bugfix
 docs/changes/newsfragments/277.misc
+docs/changes/newsfragments/278.bugfix
+docs/changes/newsfragments/279.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst