Unit tests

Author: estenhl

README.md

@@ -72,8 +72,8 @@ Running our prebuilt ```sfcn-reg-predict-brain-age```-container can be done via
 docker run \
       --rm \
       --name predict-brain-age \
-      --mount type=bind,source=/Users/esten/images,target=/images \
-      --mount type=bind,source=/Users/esten/preds,target=/predictions \
+      --mount type=bind,source=<path-to-folder-with-images>,target=/images \
+      --mount type=bind,source=<path-to-folder-with-predictions>,target=/predictions \
       estenhl/sfcn-reg-predict-brain-age
 ```
 
@@ -94,8 +94,23 @@ docker run \
       -it \
       --rm \
       --mount type=bind,source=/Users/esten/freesurfer-license.txt,target=/usr/local/freesurfer/license.txt \
-      --mount type=bind,source=/Users/esten/tmp/images/tmp.nii.gz,target=/tmp.nii.gz \
+      --mount type=bind,source=<path-to-example-image>,target=/tmp.nii.gz \
       estenhl/freesurfer:5.3
 mkdir subjects
 recon-all -sd subjects -s tmp -i /tmp.nii.gz -autorecon1
+```
+### 2. Build a FreeSurfer and FSL container
+```
+docker build \
+      --tag estenhl/freesurfer_and_fsl:6.0 \
+      --file docker/Dockerfile.freesurfer_and_fsl .
+```
+
+### 2b. Test the FreeSurfer and FSL container
+Test the FSL-portion of the container by running flirt
+```
+flirt \
+      -in tmp.nii.gz \
+      -out flirted.nii.gz \
+      -ref /usr/local/fsl/data/linearMNI/MNI152lin_T1_1mm_brain.nii.gz
 ```

docker/Dockerfile.freesurfer_and_fsl

@@ -1,7 +1,7 @@
 FROM estenhl/freesurfer:5.3
 
 RUN yum update
-RUN yum -y install bc dc git libopenblas python tar unzip wget
+RUN yum -y install bc dc git libopenblas python tar unzip wget file libquadmath
 RUN curl -sL https://rpm.nodesource.com/setup_10.x | bash -
 RUN yum -y install nodejs npm
 RUN yum clean all
@@ -11,13 +11,12 @@ RUN npm install -gq bids-validator
 
 RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py 
 RUN chmod 755 /fslinstaller.py
-#RUN /fslinstaller.py -d /usr/local/fsl -q
+RUN /fslinstaller.py -d /usr/local/fsl -q
 
-#ENV FSLDIR=/usr/local/fsl
-#ENV PATH=$FSLDIR/bin:$PATH
-#RUN /bin/bash -c 'source /usr/local/fsl/etc/fslconf/fsl.sh'
-#ENV FSLMULTIFILEQUIT=TRUE
-#ENV FSLOUTPUTTYPE=NIFTI_GZ
-#RUN ln -s /usr/local/fsl/bin/eddy_openmp /usr/local/fsl/bin/eddy
+ENV FSLDIR=/usr/local/fsl
+ENV PATH=$FSLDIR/bin:$PATH
+RUN /bin/bash -c 'source /usr/local/fsl/etc/fslconf/fsl.sh'
+ENV FSLMULTIFILEQUIT=TRUE
+ENV FSLOUTPUTTYPE=NIFTI_GZ
 
 CMD bash

notebooks/Download and preprocess IXI.ipynb

@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "id": "c86bc653",
    "metadata": {},
    "source": [
     "## 0. Configure paths and URLs"
@@ -10,6 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "bfbb419a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -34,6 +36,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "45a3f9e7",
    "metadata": {},
    "source": [
     "## 1. Setup folder structure and ensure all necessary software and packages is installed"
@@ -42,6 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "87ad8b9a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,6 +70,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "fea34c9b",
    "metadata": {},
    "source": [
     "## 2. Download, extract and reorganize the data"
@@ -74,6 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "d8322ab2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -113,6 +119,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "aec8d830",
    "metadata": {},
    "source": [
     "## 3. Preprocess the data"
@@ -121,6 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "48f0b9ad",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -136,6 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "52b2e554",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,6 +177,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "469a67c7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -190,6 +200,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "86837eca",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -212,6 +223,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "1e8fa9d4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -234,6 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "5f4d1cb0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -258,6 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "57dbe8d7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -272,6 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "398a46fe",
    "metadata": {},
    "outputs": [],
    "source": []

pyment/callbacks/__init__.py

@@ -1 +1 @@
-from .resetter import Resettable
+from .resetter import Resettable, Resetter

pyment/callbacks/resetter.py

@@ -17,6 +17,8 @@ class Resetter(Callback):
     def __init__(self, obj: Resettable):
         super().__init__()
 
+        assert isinstance(obj, Resettable)
+
         self.obj = obj
 
     def on_epoch_end(self, *args, **kwargs) -> None:

pyment/data/datasets/dataset.py

@@ -7,6 +7,9 @@ class Dataset(ABC):
     @abstractproperty
     def y(self) -> np.ndarray:
         """Returns the target vector of the dataset"""
+        pass
 
-    def __len__(self):
-        return len(self.y)
+    @abstractproperty
+    def __len__(self) -> int:
+        """Returns length of the dataset"""
+        pass

pyment/data/datasets/nifti_dataset.py

@@ -62,7 +62,7 @@ def from_folder(cls, root: str, *, images: str = 'images',
 
     @property
     def variables(self):
-        if len(self._labels) == 0:
+        if self._labels is None or len(self._labels) == 0:
             return []
 
         return list(self._labels.keys())
@@ -111,4 +111,7 @@ def __init__(self, paths: np.ndarray,
                  target: str = None) -> NiftiDataset:
         self._paths = paths
         self._labels = labels
-        self.target = target
+        self.target = target
+
+    def __len__(self) -> int:
+        return len(self.paths)

pyment/utils/preprocessing/freesurfer.py

@@ -76,6 +76,9 @@ def run(self):
 
 def convert_mgz_to_nii_gz(src: str, dest: str, *, 
                           silence: bool = True) -> None:
+    assert src.endswith('mgz'), ('First argument to convert_mgz_to_nii_gz '
+                                 'be an mgz-file')
+
     logger.debug(f'Running convert on {src}')
 
     cmd = f'mri_convert {src} {dest} -ot nii'

pyment/utils/preprocessing/fsl.py

@@ -32,15 +32,18 @@ def reorient2std_folder(src: str, dest: str, *, silence: bool = True):
                      silence=silence)
 
 
-def flirt(src: str, dest: str, *, template: str, silence: bool = True):
+def flirt(src: str, dest: str, *, template: str, 
+          degrees_of_freedom: int = 6, silence: bool = True):
     logger.debug(f'Running flirt on {src} with template {template}')
 
-    cmd = f'flirt -in {src} -out {dest} -ref {template} -dof 6'
+    cmd = (f'flirt -in {src} -out {dest} -ref {template} '
+           f'-dof {degrees_of_freedom}')
 
     run(cmd, silence=silence)
 
 
-def flirt_folder(src: str, dest: str, *, template: str, silence: bool = True):
+def flirt_folder(src: str, dest: str, *, template: str, 
+                 degrees_of_freedom: int = 6, silence: bool = True):
     if not os.path.isdir(dest):
         os.makedirs(dest)
 
@@ -52,4 +55,4 @@ def flirt_folder(src: str, dest: str, *, template: str, silence: bool = True):
             continue
 
         flirt(os.path.join(src, filename), path, template=template, 
-              silence=silence)
+              silence=silence, degrees_of_freedom=degrees_of_freedom)

requirements.txt

@@ -1,5 +1,6 @@
 jupyterlab==3.2.1
 matplotlib==3.4.3
+mock==4.0.3
 nibabel==3.2.1
 pandas==1.3.4
 pytest==6.2.4