Small but important pre-release fixes

FastSurferCNN/data_loader/conform.py

@@ -16,7 +16,6 @@
 
 # IMPORTS
 import argparse
-import logging
 import sys
 from collections.abc import Iterable
 from enum import Enum
@@ -26,6 +25,7 @@
 import numpy as np
 import numpy.typing as npt
 
+from FastSurferCNN.utils import logging
 from FastSurferCNN.utils.arg_types import VoxSizeOption
 from FastSurferCNN.utils.arg_types import float_gt_zero_and_le_one as __conform_to_one_mm
 from FastSurferCNN.utils.arg_types import target_dtype as __target_dtype
@@ -72,14 +72,14 @@ class Criteria(Enum):
 DEFAULT_CRITERIA = frozenset(DEFAULT_CRITERIA_DICT.values())
 
 
-def options_parse():
+def make_parser() -> argparse.ArgumentParser:
     """
-    Command line option parser.
+    Create an Argument parser for the conform script.
 
     Returns
     -------
-    options
-        Object holding options.
+    argparse.ArgumentParser
+        The parser object.
     """
     parser = argparse.ArgumentParser(usage=HELPTEXT)
     parser.add_argument(
@@ -172,7 +172,25 @@ def options_parse():
         action="store_true",
         help="If verbose, more specific messages are printed",
     )
-    args = parser.parse_args()
+    parser.add_argument(
+        "--log",
+        dest="logfile",
+        default="",
+        action="store",
+        help="If specified, a log file that is written to",
+    )
+    return parser
+
+def options_parse():
+    """
+    Command line option parser.
+
+    Returns
+    -------
+    options
+        Object holding options.
+    """
+    args = make_parser().parse_args()
     if args.input is None:
         raise RuntimeError("ERROR: Please specify input image")
     if not args.check_only and args.output is None:
@@ -973,6 +991,8 @@ def check_affine_in_nifti(
     except RuntimeError as e:
         sys.exit(*e.args)
 
+    logging.setup_logging(options.logfile) # logging to only the console
+
     print(f"Reading input: {options.input} ...")
     image = nib.load(options.input)
 

brun_fastsurfer.sh

@@ -439,8 +439,9 @@ function run_single()
   elif [[ -n "$statusfile" ]] && [[ "$do_surf" == 1 ]] && [[ "$do_seg" == 0 ]]
   then
     ## if status in statusfile is "Failed" last, skip this
-    IFS=" "
-    while IFS='' read -r line ; do
+    prev_ifs="$IFS" ; IFS=''
+    while read -r line ; do
+      IFS=" "
       subject="$(echo "$line" | cut -d" " -f1)"
       if [[ "$subject" == "$subject_id:" ]] ; then
         statustext="${line:$((${#subject} + 1))}"
@@ -449,7 +450,9 @@ function run_single()
           status=success
         fi
       fi
+      IFS=""
     done < "$statusfile"
+    IFS="$prev_ifs"
     if [[ "$status" == "failed" ]]
     then
       echo "INFO: Skipping $subject_id's surface recon because the segmentation failed."
@@ -512,6 +515,7 @@ function process_by_token()
   do
     if [[ "$read_in" == 1 ]]
     then
+      IFS=""
       read -r -t "$timeout_read_token" line
       returncode="$?"
       if [[ "$returncode" == 1 ]] ; then read_in=0 # EOF, terminate looking at for input
@@ -609,7 +613,8 @@ function process_by_token()
 
 function filter_token()
 {
-  while IFS='' read -r line ; do if [[ "${line:0:17}" != "#@#!NEXT-SUBJECT:" ]] ; then echo "$line" ; fi ; done
+  IFS=""
+  while read -r line ; do if [[ "${line:0:17}" != "#@#!NEXT-SUBJECT:" ]] ; then echo "$line" ; fi ; done
 }
 
 

recon_surf/README.md

@@ -18,17 +18,14 @@ bias-field corrected image and the bias-field correction is skipped.
 Usage
 =====
 
-```
-{command-output} ./recon_surf.sh --help
-```
 The *recon_surf* directory contains scripts to run the analysis. In addition, a working installation of __FreeSurfer__ 
 (the supported version, usually the most recent) is needed for a native install (or use our Docker/Singularity images). 
 
 The main script is called `recon-surf.sh` which accepts certain arguments via the command line.
 List them by running the following command:
 
-```bash
-./recon-surf.sh --help
+```{command-output} ./recon-surf.sh --help
+:cwd: /../recon_surf/
 ```
 
 Required arguments

recon_surf/recon-surf.sh

@@ -460,11 +460,11 @@ if [ "$CONFORM_LF" != /dev/null ] ; then  rm -f "$CONFORM_LF" ; fi
 echo "Log file for Conform test" > "$CONFORM_LF"
 
 # check for input conformance
-cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $t1 --check_only --vox_size min --verbose"
-RunIt "$cmd" "$LF" 2>&1 | tee -a "$CONFORM_LF"
+cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $t1 --check_only --vox_size min --verbose --log $CONFORM_LF"
+RunIt "$cmd" "$LF"
 
 # look into the CONFORM_LF to find the voxel sizes, the second conform.py call will check the legality of vox_size
-vox_size=$(grep -E " - Voxel Size " "$CONFORM_LF" | cut -d' ' -f5 | cut -d'x' -f1)
+vox_size=$(grep -oP '(?<= - Voxel Size )[0-9\.]+' "$CONFORM_LF")
 # remove the temporary conform_log (all info is also in the recon-surf logfile)
 if [ -f "$CONFORM_LF" ]; then rm -f "$CONFORM_LF" ; fi
 

run_fastsurfer.sh

@@ -822,7 +822,16 @@ then
 fi
 
 pushd "${sd}/${subject}" > /dev/null || { echo "Could not access ${sd}/${subject}!" ; exit 1 ; }
-  mapfile -t content_of_subject_dir < <(find "." -type f)
+  function filter_log_build()
+  {
+    # filter expected files $LF and scripts/BUILD.log
+    IFS=""
+    while read -r file ; do
+      if [[ "${sd}/${subject}/${file:2}" != "$seg_log" ]] && [[ "$file" != "./scripts/BUILD.log" ]] ; then echo "$file" ; fi
+    done
+  }
+
+  mapfile -t content_of_subject_dir < <(find "." -type f | filter_log_build)
 popd > /dev/null || exit 1
 if [[ "${#content_of_subject_dir[@]}" -gt 1 ]] ; then
   if [[ "$edits" == "true" ]] ; then LABEL="INFO" ; else LABEL="WARNING" ; fi

stools.sh

@@ -360,7 +360,7 @@ function make_copy_job ()
   fi
   {
     echo "#!/bin/bash"
-    echo "set -e"
+    echo "IFS=''"
     echo "mkdir -p $hpc_work/cases"
     echo "while read subject; do"
     echo "  subject_id=\$(echo \"\$subject\" | cut -d= -f1)"
@@ -412,10 +412,12 @@ function prepend ()
 {
   #param1 string to prepend to every line
   # https://serverfault.com/questions/72744/command-to-prepend-string-to-each-line
+  IFS=""
   while read -r line ; do echo "${1}${line}" ; done
 }
 function append ()
 {
   #param1 string to append to every line
+  IFS=""
   while read -r line ; do echo "${line}$1" ; done
 }