Merge pull request #249 from SyneRBI/fix-working-path

add & fix `exercises_working_path`

Author: KrisThielemans

lib/sirf_exercises/__init__.py

@@ -38,9 +38,10 @@ def exercises_data_path(*data_type):
     return os.path.join(data_path, *data_type)
 
 
-def cd_to_working_dir(*subfolders):
+
+def exercises_working_path(*subfolders):
     '''
-    Creates and changes the current directory to a working directory for the
+    Creates and returns the working directory for the
     current exercise, based on the argument(s). If multiple
     strings are given, they will be treated as subdirectories.
 
@@ -56,5 +57,9 @@ def cd_to_working_dir(*subfolders):
     except ImportError:
         working_dir = exercises_data_path('working_folder', *subfolders)
     os.makedirs(working_dir, exist_ok=True)
-    os.chdir(working_dir)
+    return working_dir
 
+
+def cd_to_working_dir(*subfolders):
+    '''Same as os.chdir(exercises_working_path(*subfolders))'''
+    os.chdir(exercises_working_path(*subfolders))

notebooks/Synergistic/BrainWeb.ipynb

@@ -70,13 +70,11 @@
     "import sirf.Reg as reg\n",
     "from math import cos, sin, pi\n",
     "from sirf.Utilities import examples_data_path\n",
-    "from sirf_exercises import exercises_data_path\n",
+    "from sirf_exercises import cd_to_working_dir\n",
     "import shutil\n",
     "from scipy.ndimage import gaussian_filter\n",
     "\n",
-    "wd = exercises_data_path('working_folder', 'Synergistic', 'BrainWeb')\n",
-    "makedirs(wd, exist_ok=True)\n",
-    "chdir(wd)"
+    "cd_to_working_dir('Synergistic', 'BrainWeb')"
    ]
   },
   {

notebooks/Synergistic/Dual_PET.ipynb

@@ -96,7 +96,7 @@
    "outputs": [],
    "source": [
     "# copy files to working folder and change directory to where the output files are\n",
-    "brainweb_sim_data_path = exercises_data_path('working_folder', 'Synergistic', 'BrainWeb')\n",
+    "brainweb_sim_data_path = exercises_working_path('Synergistic', 'BrainWeb')\n",
     "\n",
     "fname_FDG_sino = os.path.join(brainweb_sim_data_path, 'FDG_sino_noisy.hs')\n",
     "fname_FDG_uMap = os.path.join(brainweb_sim_data_path, 'uMap_small.hv')\n",

notebooks/Synergistic/HKEM_reconstruction.ipynb

@@ -101,9 +101,9 @@
     "#import scipy\n",
     "#from scipy import optimize\n",
     "import sirf.STIR as pet\n",
-    "from sirf_exercises import exercises_data_path\n",
+    "from sirf_exercises import exercises_working_path\n",
     "\n",
-    "brainweb_sim_data_path = exercises_data_path('working_folder', 'Synergistic', 'BrainWeb')"
+    "brainweb_sim_data_path = exercises_working_path('Synergistic', 'BrainWeb')"
    ]
   },
   {

notebooks/Synergistic/MAPEM_Bowsher.ipynb

@@ -75,9 +75,9 @@
     "from scipy.ndimage.filters import gaussian_filter\n",
     "import sirf.STIR as pet\n",
     "from numba import jit\n",
-    "from sirf_exercises import exercises_data_path\n",
+    "from sirf_exercises import exercises_working_path\n",
     "\n",
-    "brainweb_sim_data_path = exercises_data_path('working_folder', 'Synergistic', 'BrainWeb')\n",
+    "brainweb_sim_data_path = exercises_working_path('Synergistic', 'BrainWeb')\n",
     "# set-up redirection of STIR messages to files\n",
     "msg_red = pet.MessageRedirector('info.txt', 'warnings.txt', 'errors.txt')\n",
     "# plotting settings\n",