Improve Mac support and clean up dependencies

FastSurferCNN/segstats.py

@@ -725,7 +725,7 @@ def read_classes_from_lut(lut_file: str | Path):
     }
     return pd.read_csv(
         lut_file,
-        delim_whitespace=True,
+        sep='\s+',
         index_col=False,
         skip_blank_lines=True,
         comment="#",

FastSurferCNN/utils/mapper.py

@@ -999,7 +999,7 @@ def __init__(
 
         self._data = pandas.read_csv(
             file_or_buffer,
-            delim_whitespace=True,
+            sep='\s+',
             index_col=0,
             skip_blank_lines=True,
             comment="#",

doc/overview/INSTALL.md

@@ -165,19 +165,17 @@ Continue with the example in [Example 1](EXAMPLES.md#example-1-fastsurfer-docker
 
 ### Native
 
-On modern Macs with the Apple Silicon M1 or M2 ARM-based chips, we recommend a native installation as it runs much faster than Docker in our tests. The experimental support for the built-in AI Accelerator is also only available on native installations. Native installation also supports older Intel chips.
+On modern Macs with the Apple Silicon M1 or M2 ARM-based chips, we recommend a native installation as it runs much faster than Docker in our tests. The experimental support for the built-in AI accelerator (MPS) is also only available on native installations. Native installation also supports older Intel chips.
 
 #### 1. Git and Bash
-If you do not have git and a recent bash (version > 4.0 required!) installed, install them via the packet manager, e.g. brew.
+If you do not have git you can install it via the packet manager, e.g. brew.
 This installs brew and then bash:
 
 ```sh
 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
-brew install bash
+brew install git
 ```
 
-Make sure you use this bash and not the older one provided with MacOS!
-
 #### 2. Python
 Create a python environment, activate it, and upgrade pip. Here we use pip, but you should also be able to use conda for python: 
 
@@ -195,7 +193,6 @@ cd FastSurfer
 export PYTHONPATH="${PYTHONPATH}:$PWD"
 ```
 
-
 Install the FastSurfer requirements
 ```sh
 python3 -m pip install -r requirements.mac.txt
@@ -215,14 +212,12 @@ You can also download all network checkpoint files (this should be done if you a
 python3 FastSurferCNN/download_checkpoints.py --all
 ```
 
-Once all dependencies are installed, run the FastSurfer segmentation only (!!) by calling ```bash ./run_fastsurfer.sh --seg_only ....``` with the appropriate command line flags, see the [commandline documentation](../../README.md#usage). 
-
-Note: You may always need to prepend the command with `bash` (i.e. `bash run_fastsurfer.sh <...>`) to ensure that bash 4.0 is used instead of the system default.
+Once all dependencies are installed, you can run the FastSurfer segmentation only by calling ```./run_fastsurfer.sh --seg_only ....``` with the appropriate command line flags, see the [commandline documentation](../../README.md#usage). 
 
-To run the full pipeline, install and source also the supported FreeSurfer version according to their [Instructions](https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads). There is a freesurfer email list, if you run into problems during this step.
+To run the full pipeline, install and source also the supported FreeSurfer version according to their [Instructions](https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads). There is a freesurfer email list, if you run into problems during this step. Note, that currently FreeSurfer for MacOS supports no ARM, but only Intel, so on modern M-chips it might be slow due to the emulation.
 
 #### 4. Apple AI Accelerator support
-You can also try the experimental support for the Apple Silicon AI Accelerator by setting `PYTORCH_ENABLE_MPS_FALLBACK` and passing `--device mps`:
+You can also try the experimental support for the Apple Silicon AI Accelerator by setting `PYTORCH_ENABLE_MPS_FALLBACK` and passing `--device mps` for the segmentation module to make use of the fast GPU:
 
 ```sh
 export PYTORCH_ENABLE_MPS_FALLBACK=1

pyproject.toml

@@ -32,20 +32,22 @@ classifiers = [
 ]
 dependencies = [
     'h5py>=3.7',
-    'lapy>=0.4.1',
-    'matplotlib>=3.5.1',
-    'nibabel>=3.2.2',
-    'numpy>=1.21',
-    'pandas>=1.4.3',
-    'torch>=1.12.0',
+    'lapy>=1.0.1',
+    'matplotlib>=3.7.1',
+    'nibabel>=5.1.0',
+    'numpy>=1.25,<2',
+    'pandas>=1.5.3',
     'pyyaml>=6.0',
-    'scipy>=1.8.0',
-    'yacs>=0.1.8',
-    'simpleitk>=2.1.1',
-    'scipy>=1.8.0',
-    'tensorboard>=2.9.1',
+    'scikit-image>=0.19.3',
+    'scikit-learn>=1.2.2',
+    'scipy>=1.10.1,!=1.13.0',
+    'simpleitk>=2.2.1',
+    'tensorboard>=2.12.1',
+    'torch>=2.0.1',
     'torchio>=0.18.83',
-    'tqdm>=4.64',
+    'torchvision>=0.15.2',
+    'tqdm>=4.65',
+    'yacs>=0.1.8',
 ]
 
 [project.optional-dependencies]

recon_surf/functions.sh

@@ -30,12 +30,13 @@ function RunIt()
   if [[ $# -eq 3 ]]
   then
     local CMDF=$3
-    echo "echo ${cmd@Q}" |& tee -a $CMDF
-    echo "$timecmd $cmd" |& tee -a $CMDF
+    printf -v tmp %q "$cmd"
+    echo "echo $tmp" 2>&1 | tee -a $CMDF
+    echo "$timecmd $cmd" 2>&1 | tee -a $CMDF
     echo "if [ \${PIPESTATUS[0]} -ne 0 ] ; then exit 1 ; fi" >> $CMDF
   else
-    echo $cmd |& tee -a $LF
-    $timecmd $cmd |& tee -a $LF
+    echo $cmd 2>&1 | tee -a $LF
+    $timecmd $cmd 2>&1 | tee -a $LF
     if [ ${PIPESTATUS[0]} -ne 0 ] ; then exit 1 ; fi
   fi
 }
@@ -107,21 +108,21 @@ function softlink_or_copy()
   if [[ $# -eq 4 ]]
   then
     local CMDF=$4
-    echo "echo \"$ln_cmd\" " |& tee -a $CMDF
-    echo "$timecmd $ln_cmd " |& tee -a $CMDF
-    echo "if [ \${PIPESTATUS[0]} -ne 0 ]" |& tee -a $CMDF
-    echo "then " |& tee -a $CMDF
-    echo "  echo \"$cp_cmd\" " |& tee -a $CMDF
-    echo "  $timecmd $cp_cmd " |& tee -a $CMDF
+    echo "echo \"$ln_cmd\" " 2>&1 | tee -a $CMDF
+    echo "$timecmd $ln_cmd " 2>&1 | tee -a $CMDF
+    echo "if [ \${PIPESTATUS[0]} -ne 0 ]" 2>&1 | tee -a $CMDF
+    echo "then " 2>&1 | tee -a $CMDF
+    echo "  echo \"$cp_cmd\" " 2>&1 | tee -a $CMDF
+    echo "  $timecmd $cp_cmd " 2>&1 | tee -a $CMDF
     echo "  if [ \${PIPESTATUS[0]} -ne 0 ] ; then exit 1 ; fi" >> $CMDF
-    echo "fi" |& tee -a $CMDF
+    echo "fi" 2>&1 | tee -a $CMDF
   else
-    echo $ln_cmd |& tee -a $LF
-    $timecmd $ln_cmd |& tee -a $LF
+    echo $ln_cmd 2>&1 | tee -a $LF
+    $timecmd $ln_cmd 2>&1 | tee -a $LF
     if [ ${PIPESTATUS[0]} -ne 0 ]
     then
-      echo $cp_cmd |& tee -a $LF
-      $timecmd $cp_cmd |& tee -a $LF
+      echo $cp_cmd 2>&1 | tee -a $LF
+      $timecmd $cp_cmd 2>&1 | tee -a $LF
       if [ ${PIPESTATUS[0]} -ne 0 ] ; then exit 1 ; fi
     fi
   fi