Merge pull request SyneRBI#101 from ashgillman/working_dir

Add `cd_to_working_dir` function and use it. Fixes SyneRBI#84
johannesmayer · Jun 17, 2021 · 033a03e · 033a03e
2 parents 24d94f1 + 5926ddf
commit 033a03e
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diff --git a/lib/sirf_exercises/__init__.py b/lib/sirf_exercises/__init__.py
@@ -15,6 +15,7 @@
 
 import os
 
+
 def exercises_data_path(*data_type):
     '''
     Returns the path to data used by SIRF-exercises.
@@ -32,6 +33,23 @@ def exercises_data_path(*data_type):
     if data_path is None or not os.path.exists(data_path):
         raise RuntimeError(
             "Exercises data weren't found. Please run download_data.sh in the "
-            "scripts directory")
+            "scripts directory (use its -h option to get help)")
+
+    return os.path.join(data_path, *data_type)
 
-    return os.path.join(data_path, *data_type)
+
+def cd_to_working_dir(*subfolders):
+    '''
+    Creates and changes the current directory to a working directory for the
+    current exercise, based on the argument(s). If multiple
+    strings are given, they will be treated as subdirectories.
+
+    Implementation detail: this is defined as
+    {exercises_data_path()}/working_folder/{subfolders[0]}/{subfolders[1]}/...
+
+    subfolders: the path will include this.
+    Multiple arguments can be given for nested subdirectories.
+    '''
+    working_dir = exercises_data_path('working_folder', *subfolders)
+    os.makedirs(working_dir, exist_ok=True)
+    os.chdir(working_dir)
diff --git a/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb b/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb
@@ -54,7 +54,10 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('Introductory', 'acquisition_model_mr_pet_ct')"
    ]
   },
   {

diff --git a/notebooks/Introductory/introduction.ipynb b/notebooks/Introductory/introduction.ipynb
@@ -63,6 +63,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# We have placed a file in this directory, notebook_setup.py, which will allow us to import the sirf_exercises library\n",
+    "import notebook_setup\n",
+    "\n",
+    "# The sirf_exercises defines some handy tools for these notebooks\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "\n",
     "# Initial imports etc\n",
     "import numpy\n",
     "from numpy.linalg import norm\n",
@@ -77,6 +83,16 @@
     "from sirf.Utilities import examples_data_path"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Move to a working directory for this notebook\n",
+    "cd_to_working_dir('Introductory', 'introduction')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -716,15 +732,6 @@
    "display_name": "Python 3",
    "language": "python",
    "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython"
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/MR/a_fully_sampled.ipynb b/notebooks/MR/a_fully_sampled.ipynb
@@ -156,7 +156,12 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "\n",
+    "# Setup the working directory for the notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('MR', 'a_fully_sampled')"
    ]
   },
   {
@@ -166,7 +171,6 @@
    "outputs": [],
    "source": [
     "__version__ = '0.1.0'\n",
-    "import notebook_setup  # set exercises path\n",
     "\n",
     "# import engine module\n",
     "import sirf.Gadgetron as pMR\n",
@@ -175,11 +179,7 @@
     "# import further modules\n",
     "import os\n",
     "import matplotlib.pyplot as plt\n",
-    "from sirf_exercises import exercises_data_path\n",
-    "\n",
-    "#%% GO TO MR FOLDER\n",
-    "acrphantom_data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
-    "os.chdir(acrphantom_data_path)"
+    "from sirf_exercises import exercises_data_path"
    ]
   },
   {
@@ -198,7 +198,8 @@
    "outputs": [],
    "source": [
     "#%% LOAD RAW MR DATA\n",
-    "filename = 'ptb_resolutionphantom_fully_ismrmrd.h5' \n",
+    "data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
+    "filename = os.path.join(data_path, 'ptb_resolutionphantom_fully_ismrmrd.h5')\n",
     "acq_data = pMR.AcquisitionData(filename)\n",
     "\n",
     "print(type(acq_data))"
@@ -461,5 +462,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/MR/b_kspace_filter.ipynb b/notebooks/MR/b_kspace_filter.ipynb
@@ -49,7 +49,12 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "\n",
+    "# Setup the working directory for the notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('MR', 'b_kspace_filter')"
    ]
   },
   {
@@ -60,8 +65,6 @@
    "source": [
     "__version__ = '0.1.0'\n",
     "\n",
-    "import notebook_setup\n",
-    "\n",
     "# import engine module\n",
     "import sirf.Gadgetron as pMR\n",
     "from sirf.Utilities import examples_data_path\n",
@@ -70,11 +73,7 @@
     "# import further modules\n",
     "import os, numpy\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "#%% GO TO MR FOLDER\n",
-    "acrphantom_data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
-    "os.chdir(acrphantom_data_path)"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -166,7 +165,9 @@
     "\n",
     "\n",
     "\n",
-    "acq_data = pMR.AcquisitionData('ptb_resolutionphantom_fully_ismrmrd.h5')\n",
+    "data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
+    "filename = os.path.join(data_path, 'ptb_resolutionphantom_fully_ismrmrd.h5')\n",
+    "acq_data = pMR.AcquisitionData(filename)\n",
     "\n",
     "kdim = acq_data.dimensions()\n",
     "print('Size of k-space %dx%dx%d' % kdim)"

diff --git a/notebooks/MR/c_coil_combination.ipynb b/notebooks/MR/c_coil_combination.ipynb
@@ -39,7 +39,12 @@
     "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
     "##   See the License for the specific language governing permissions and\n",
     "##   limitations under the License.\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "\n",
+    "# Setup the working directory for the notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('MR', 'c_coil_combination')"
    ]
   },
   {
@@ -59,20 +64,14 @@
    "source": [
     "__version__ = '0.1.0'\n",
     "\n",
-    "import notebook_setup\n",
-    "\n",
     "# import engine module\n",
     "import sirf.Gadgetron as pMR\n",
     "from sirf.Utilities import examples_data_path\n",
     "from sirf_exercises import exercises_data_path\n",
     "\n",
     "# import further modules\n",
     "import os, numpy\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "#%% GO TO MR FOLDER\n",
-    "acrphantom_data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
-    "os.chdir(acrphantom_data_path)"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -112,7 +111,8 @@
    "outputs": [],
    "source": [
     "#%% LOAD AND PREPROCESS RAW MR DATA\n",
-    "filename = 'ptb_resolutionphantom_fully_ismrmrd.h5'\n",
+    "data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
+    "filename = os.path.join(data_path, 'ptb_resolutionphantom_fully_ismrmrd.h5')\n",
     "acq_data = pMR.AcquisitionData(filename)\n",
     "preprocessed_data = pMR.preprocess_acquisition_data(acq_data)\n",
     "preprocessed_data.sort()\n",

diff --git a/notebooks/MR/d_undersampled_reconstructions.ipynb b/notebooks/MR/d_undersampled_reconstructions.ipynb
@@ -49,7 +49,12 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "\n",
+    "# Setup the working directory for the notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('MR', 'd_undersampled_reconstructions')"
    ]
   },
   {
@@ -59,7 +64,6 @@
    "outputs": [],
    "source": [
     "__version__ = '0.1.0'\n",
-    "import notebook_setup\n",
     "\n",
     "# import engine module\n",
     "import sirf.Gadgetron as pMR\n",
@@ -72,11 +76,7 @@
     "import matplotlib.pyplot as plt\n",
     "import matplotlib.animation as animation\n",
     "\n",
-    "from tqdm.auto import trange\n",
-    "\n",
-    "#%% GO TO MR FOLDER\n",
-    "acrphantom_data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
-    "os.chdir(acrphantom_data_path)"
+    "from tqdm.auto import trange"
    ]
   },
   {
@@ -206,7 +206,8 @@
     "\n",
     "\n",
     "\n",
-    "filename_full_file = 'ptb_resolutionphantom_fully_ismrmrd.h5'\n",
+    "data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')\n",
+    "filename_full_file = os.path.join(data_path, 'ptb_resolutionphantom_fully_ismrmrd.h5')\n",
     "\n",
     "full_acq_data = pMR.AcquisitionData(filename_full_file)\n",
     "prep_full_data = pMR.preprocess_acquisition_data(full_acq_data)\n",
@@ -242,7 +243,7 @@
    "outputs": [],
    "source": [
     "# LOADING AND PREPROCESSING DATA FOR THIS SET\n",
-    "filename_grappa_file = 'ptb_resolutionphantom_GRAPPA4_ismrmrd.h5'\n",
+    "filename_grappa_file = os.path.join(data_path, 'ptb_resolutionphantom_GRAPPA4_ismrmrd.h5')\n",
     "acq_data = pMR.AcquisitionData(filename_grappa_file)\n",
     "preprocessed_data = pMR.preprocess_acquisition_data(acq_data)\n",
     "preprocessed_data.sort()\n"

diff --git a/notebooks/MR/e_advanced_recon.ipynb b/notebooks/MR/e_advanced_recon.ipynb
@@ -53,7 +53,12 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib notebook\n",
+    "\n",
+    "# Setup the working directory for the notebook\n",
+    "import notebook_setup\n",
+    "from sirf_exercises import cd_to_working_dir\n",
+    "cd_to_working_dir('MR', 'e_advanced_recon')"
    ]
   },
   {
@@ -64,8 +69,6 @@
    "source": [
     "__version__ = '0.1.1'\n",
     "\n",
-    "import notebook_setup\n",
-    "\n",
     "# import engine module\n",
     "import sirf.Gadgetron as pMR\n",
     "\n",
@@ -85,8 +88,7 @@
    "outputs": [],
    "source": [
     "from sirf_exercises import exercises_data_path\n",
-    "#%% GO TO MR FOLDER\n",
-    "os.chdir(exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA'))"
+    "data_path = exercises_data_path('MR', 'PTB_ACRPhantom_GRAPPA')"
    ]
   },
   {
@@ -121,7 +123,7 @@
    "outputs": [],
    "source": [
     "# LOADING AND PREPROCESSING DATA FOR THIS SET\n",
-    "filename_grappa_file = 'ptb_resolutionphantom_GRAPPA4_ismrmrd.h5'\n",
+    "filename_grappa_file = os.path.join(data_path, 'ptb_resolutionphantom_GRAPPA4_ismrmrd.h5')\n",
     "acq_data = pMR.AcquisitionData(filename_grappa_file)\n",
     "preprocessed_data = pMR.preprocess_acquisition_data(acq_data)\n",
     "preprocessed_data.sort()\n",