junifer 0.0.4.dev422__py3-none-any.whl → 0.0.4.dev428__py3-none-any.whl

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/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/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/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/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.dist-info → junifer-0.0.4.dev428.dist-info}/METADATA

@@ -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.dist-info → junifer-0.0.4.dev428.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=VbLPpJqcmJrzHXvf0BHgEpdwrb1OfYXv6YQumRhXsiE,428
+junifer/_version.py,sha256=jT7gbO6ktFrS562Be3j_xFtAYFgfUYL_mi1L5XMu5Kc,428
 junifer/stats.py,sha256=KUX4jJcLWnlE34coet8EkdFypFd-td4Vtpx5LvlomVs,5879
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
@@ -12,13 +12,13 @@ junifer/api/res/afni/3dAFNItoNIFTI,sha256=Fsy5S5rwIBb1MepLfl_5FQhE7gv6NDwNyAR_k0
 junifer/api/res/afni/3dRSFC,sha256=MkPtS_nKEoJOHDAT3ZP9IA-SvMdhyzZDiyxObV_XI3g,44
 junifer/api/res/afni/3dReHo,sha256=Jb5B97iPPPQ14zAz7tK5BVG4jPZyOe9c6kgM6ixKaY8,44
 junifer/api/res/afni/afni,sha256=idLvNWHwd6P4jWXfk6hMXQckdpcTJYbvnLC3uNP6sBg,42
-junifer/api/res/afni/run_afni_docker.sh,sha256=Qw_yLv7GijmjPmmuiDA0qRmB2Kxuvsoerm5R7mjtzZo,1106
+junifer/api/res/afni/run_afni_docker.sh,sha256=_MHr4oEfnjvFEegx8VWl3S0Js0KioySvtJfdxyea0JE,1130
 junifer/api/res/ants/antsApplyTransforms,sha256=SqlQEJ2RMMw_qGyDaNTXKzQqO7Bvrm6y5SEPmyqHiYc,57
 junifer/api/res/ants/antsApplyTransformsToPoints,sha256=lqyvQGo8oI-RNpNlRqz-BvLHh7Th5HQgsDZjHF6nEeI,65
-junifer/api/res/ants/run_ants_docker.sh,sha256=svzsACUd1kh3C_ODL2fAUAY2fMKsjQ-MsCPOuxKxwW0,1095
+junifer/api/res/ants/run_ants_docker.sh,sha256=d6lZ9CCPP3nsCALhW4T4tI67gyUSiM4AuXj5JPKTLtA,1119
 junifer/api/res/fsl/applywarp,sha256=DBgHfsn1yXWq0t-P7J0YvrjjJNgiblwDsh9L1hF9v_w,46
 junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
-junifer/api/res/fsl/run_fsl_docker.sh,sha256=9y_9ehmVeflf0zfssXUNzaiS9FRPTXAd84XzyY5lmck,1098
+junifer/api/res/fsl/run_fsl_docker.sh,sha256=mRLtZo0OgDwleoee2MG6rYI37HVuGNk9zOADwcl97RA,1122
 junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
 junifer/api/tests/test_api_utils.py,sha256=_ykEECJN0qTEBcJ2YSvOAQrRN-xmEilRLPyirC5cO_o,2285
 junifer/api/tests/test_cli.py,sha256=qKWkAf-A1DeDwCtrOaCrQ5bmuUYcLWeRbGk2K95OMHQ,5717
@@ -40,7 +40,7 @@ junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJG
 junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=e-jdvcZ9B0mka6_573JJU_cGwSaUV54U8X_n0UadtJY,3351
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=oUjOs8_M6fitNb44izxpXf3su1e4pG_vCdjwVYkjZjQ,550
-junifer/data/coordinates.py,sha256=BVpiz9dkwTKwlAnPE8R44dIUD3gCjd9CZBDJHQR9kCY,10957
+junifer/data/coordinates.py,sha256=10bXVy94eZALfqdEbAbHTOuuF0Od9Zn2QbCFjAFSY5M,10980
 junifer/data/masks.py,sha256=chWSl-vyv5Nsd9GuQzydXPOY3AdhApOJq_42NSKpykQ,16952
 junifer/data/parcellations.py,sha256=wL8lkAYYvg7NDt160EA8N_xFjK8ZtDwoXYJQHNHwbDU,55805
 junifer/data/utils.py,sha256=K9quLIoWRmm2QFM8Rdy_5bYsWb_XhL0l5Uq_1Sie0kA,1274
@@ -225,10 +225,10 @@ junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev422.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev422.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev422.dist-info/METADATA,sha256=i9W1FfW71F5HsSe3Fd2gKrlUWMV9MY93mVc-P478nL0,7569
-junifer-0.0.4.dev422.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev422.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev422.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev422.dist-info/RECORD,,
+junifer-0.0.4.dev428.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev428.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev428.dist-info/METADATA,sha256=f6alN25QirsBK0lXfvMUvJQq8hGt7XvgXayAjn9mf2k,7569
+junifer-0.0.4.dev428.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev428.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev428.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev428.dist-info/RECORD,,