Merge pull request #5 from MEDomics-UdeS/dev

All test done, many bug fixes and version bumped
MEDomics-UdeS · Apr 14, 2024 · f0a3fb2 · f0a3fb2
2 parents fe197af + 65ae477
commit f0a3fb2
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Showing 16 changed files with 31,998 additions and 5,957 deletions.
diff --git a/MEDimage/__init__.py b/MEDimage/__init__.py
@@ -14,7 +14,7 @@
 logging.getLogger(__name__).addHandler(stream_handler)
 
 __author__ = "MEDomicsLab consortium"
-__version__ = "0.9.3"
+__version__ = "0.9.4"
 __copyright__ = "Copyright (C) MEDomicsLab consortium"
 __license__ = "GNU General Public License 3.0"
 __maintainer__ = "MAHDI AIT LHAJ LOUTFI"

diff --git a/MEDimage/learning/DataCleaner.py b/MEDimage/learning/DataCleaner.py
@@ -51,7 +51,7 @@ def cut_off_missing_per_sample(self, var_of_type: List[str], missing_cutoff : fl
         """
         # Initialization
         n_observation, n_features = self.df_features.shape
-        empty_vec = np.zeros(n_observation, dtype=np.int)
+        empty_vec = np.zeros(n_observation, dtype=int)
         data = self.df_features[var_of_type]
         empty_vec += data.isna().sum(axis=1).values
 

diff --git a/MEDimage/wrangling/DataManager.py b/MEDimage/wrangling/DataManager.py
@@ -201,10 +201,11 @@ def __associate_rt_stuct(self) -> None:
         """
         print('--> Associating all RT objects to imaging volumes')
         n_rs = len(self.__dicom.stack_path_rs)
+        self.__dicom.stack_series_rs = list(dict.fromkeys(self.__dicom.stack_series_rs))
         if n_rs:
             for i in trange(0, n_rs):
-                try: # PUT ALL THE DICOM PATHS WITH THE SAME UID IN THE SAME PATH LIST
-                    self.__dicom.stack_series_rs = list(set(self.__dicom.stack_series_rs))
+                try: 
+                    # PUT ALL THE DICOM PATHS WITH THE SAME UID IN THE SAME PATH LIST
                     ind_series_id = self.__find_uid_cell_index(
                                                         self.__dicom.stack_series_rs[i], 
                                                         self.__dicom.cell_series_id)
@@ -274,6 +275,8 @@ def __read_all_dicoms(self) -> None:
                         except:
                             frame_uid = info.FrameOfReferenceUID
                         self.__dicom.stack_frame_rs += [frame_uid]
+                    else:
+                        print("Modality not supported: ", info.Modality)
 
                 except Exception as e:
                     print(f'Error while reading: {file}, error: {e}\n')

diff --git a/environment.yml b/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - nibabel
   - pandas<2.0.0
   - pillow
-  - pydicom<2.0.0
+  - pydicom>1.2.0, <=1.3.0
   - pywavelets
   - scikit-image
   - scipy

diff --git a/notebooks/demo/Glioma-Demo.ipynb b/notebooks/demo/Glioma-Demo.ipynb
diff --git a/notebooks/ibsi/ibsi1p1.ipynb b/notebooks/ibsi/ibsi1p1.ipynb
@@ -74,14 +74,19 @@
    "execution_count": 1,
    "id": "98c17c3c",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "PyCUDA is not installed. Please install it to use the textural filters.\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import sys\n",
     "\n",
-    "MODULE_DIR = os.path.dirname(os.path.abspath('../MEDimage/'))\n",
-    "sys.path.append(os.path.dirname(MODULE_DIR))\n",
-    "\n",
     "from copy import deepcopy\n",
     "from pathlib import Path\n",
     "\n",
@@ -145,9 +150,7 @@
    "cell_type": "code",
    "execution_count": 3,
    "id": "c7ae2418",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -161,7 +164,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 2/2 [00:00<00:00, 59918.63it/s]\n"
+      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:00<00:00, 52265.47it/s]\n"
      ]
     },
     {
@@ -176,7 +179,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 1/1 [00:00<00:00, 456.60it/s]"
+      "  0%|                                                                                                                 | 0/2 [00:00<?, ?it/s]WARNING:root:The patient ID of the following file: FIG61__SEG.CTscan.npy does not respect the MEDimage naming convention 'study-institution-id' (Ex: Glioma-TCGA-001)\n",
+      "WARNING:root:The patient ID of the following file: FIG61__SEG.CTscan.npy does not respect the MEDimage naming convention 'study-institution-id' (Ex: Glioma-TCGA-001)\n",
+      "100%|████████████████████████████████████████████████████████████████████████████████████████████████████████| 2/2 [00:00<00:00, 138.29it/s]"
      ]
     },
     {
@@ -283,6 +288,7 @@
     "            mask_int=roi_obj_int.data, \n",
     "            mask_morph=roi_obj_morph.data,\n",
     "            res=MEDinstance.params.process.scale_non_text,\n",
+    "            intensity_type=\"definite\"\n",
     "        )"
    ]
   },
@@ -307,7 +313,8 @@
     "local_intensity = MEDimage.biomarkers.local_intensity.extract_all(\n",
     "            img_obj=vol_obj.data,\n",
     "            roi_obj=roi_obj_int.data,\n",
-    "            res=MEDinstance.params.process.scale_non_text)"
+    "            res=MEDinstance.params.process.scale_non_text,\n",
+    "            intensity_type=\"definite\")"
    ]
   },
   {
@@ -330,10 +337,49 @@
    "outputs": [],
    "source": [
     "stats = MEDimage.biomarkers.stats.extract_all(\n",
-    "            vol=vol_int_re\n",
+    "            vol=vol_int_re,\n",
+    "            intensity_type=\"definite\"\n",
     "        )"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "ed068427-0823-4788-ab43-dee44f728fe8",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'Fstat_mean': 2.1486487,\n",
+       " 'Fstat_var': 3.0454712,\n",
+       " 'Fstat_skew': 1.0838206041847196,\n",
+       " 'Fstat_kurt': -0.3546205634536057,\n",
+       " 'Fstat_median': 1.0,\n",
+       " 'Fstat_min': 1.0,\n",
+       " 'Fstat_P10': 1.0,\n",
+       " 'Fstat_P90': 4.0,\n",
+       " 'Fstat_max': 6.0,\n",
+       " 'Fstat_iqr': 3.0,\n",
+       " 'Fstat_range': 5.0,\n",
+       " 'Fstat_mad': 1.5522282,\n",
+       " 'Fstat_rmad': 1.1138338,\n",
+       " 'Fstat_medad': 1.1486486,\n",
+       " 'Fstat_cov': 0.8121978,\n",
+       " 'Fstat_qcod': 0.6,\n",
+       " 'Fstat_energy': 567.0,\n",
+       " 'Fstat_rms': 2.7680612}"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "stats"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "60a1bb76",
@@ -347,7 +393,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "id": "e9e53184",
    "metadata": {},
    "outputs": [],
@@ -369,7 +415,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "id": "9fc60011",
    "metadata": {},
    "outputs": [],
@@ -409,7 +455,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "id": "5bc89af2",
    "metadata": {},
    "outputs": [],
@@ -440,7 +486,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "id": "b1ba460c",
    "metadata": {},
    "outputs": [],
@@ -464,7 +510,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "id": "ffc856b0",
    "metadata": {},
    "outputs": [],
@@ -487,7 +533,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "id": "f3ab15dd",
    "metadata": {
     "scrolled": true
@@ -511,7 +557,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "id": "96a026c2",
    "metadata": {},
    "outputs": [],
@@ -534,7 +580,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "18ea2f75",
    "metadata": {},
    "outputs": [],
@@ -557,7 +603,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "id": "c7b48e08",
    "metadata": {},
    "outputs": [],
@@ -577,7 +623,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "id": "0169e310",
    "metadata": {},
    "outputs": [],
@@ -607,11 +653,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "id": "b50a025e",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -642,10 +686,10 @@
       "            \"Fmorph_a_dens_ombb\": 0.8662290845560473,\n",
       "            \"Fmorph_v_dens_aee\": 1.172817247682943,\n",
       "            \"Fmorph_a_dens_aee\": 1.3551287345086926,\n",
-      "            \"Fmorph_v_dens_mvee\": 0.43676680502143267,\n",
-      "            \"Fmorph_a_dens_mvee\": 0.7077858057685694,\n",
-      "            \"Fmorph_v_dens_conv_hull\": 0.960852043753598,\n",
-      "            \"Fmorph_a_dens_conv_hull\": 1.0328688432280573,\n",
+      "            \"Fmorph_v_dens_mvee\": 0.4487938537177223,\n",
+      "            \"Fmorph_a_dens_mvee\": 0.6963256023315707,\n",
+      "            \"Fmorph_v_dens_conv_hull\": 0.9608520437535985,\n",
+      "            \"Fmorph_a_dens_conv_hull\": 1.032868843228057,\n",
       "            \"Fmorph_integ_int\": 1195.3649150530498,\n",
       "            \"Fmorph_moran_i\": [],\n",
       "            \"Fmorph_geary_c\": []\n",
@@ -670,8 +714,8 @@
       "            \"Fstat_max\": 6.0,\n",
       "            \"Fstat_iqr\": 3.0,\n",
       "            \"Fstat_range\": 5.0,\n",
-      "            \"Fstat_mad\": 1.5522279739379883,\n",
-      "            \"Fstat_rmad\": 1.1138339042663574,\n",
+      "            \"Fstat_mad\": 1.5522282123565674,\n",
+      "            \"Fstat_rmad\": 1.1138337850570679,\n",
       "            \"Fstat_medad\": 1.1486486196517944,\n",
       "            \"Fstat_cov\": 0.8121978044509888,\n",
       "            \"Fstat_qcod\": 0.6,\n",
@@ -693,8 +737,8 @@
       "            \"Fih_mode\": 1,\n",
       "            \"Fih_iqr\": 3.0,\n",
       "            \"Fih_range\": 5.0,\n",
-      "            \"Fih_mad\": 1.5522279739379883,\n",
-      "            \"Fih_rmad\": 1.1138339042663574,\n",
+      "            \"Fih_mad\": 1.5522282123565674,\n",
+      "            \"Fih_rmad\": 1.1138337850570679,\n",
       "            \"Fih_medad\": 1.1486486196517944,\n",
       "            \"Fih_cov\": 0.8121978044509888,\n",
       "            \"Fih_qcod\": 0.6,\n",
@@ -725,7 +769,7 @@
       "                \"Fcm_joint_var\": 3.132460960144601,\n",
       "                \"Fcm_joint_entr\": 2.5738963770752696,\n",
       "                \"Fcm_diff_avg\": 1.3795066413662238,\n",
-      "                \"Fcm_diff_var\": 3.2146084852500096,\n",
+      "                \"Fcm_diff_var\": 3.21460848525001,\n",
       "                \"Fcm_diff_entr\": 1.6408766743670586,\n",
       "                \"Fcm_sum_avg\": 4.297912713472486,\n",
       "                \"Fcm_sum_var\": 7.412196781754876,\n",
@@ -873,7 +917,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,