new version for static datas

Kapoorlabs-CAPED · Jun 4, 2022 · 09ec040 · 09ec040
1 parent d178758
commit 09ec040
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Showing 7 changed files with 39 additions and 455 deletions.
diff --git a/Notebooks/MIDOG_oneat_training_data_creator.ipynb b/Notebooks/MIDOG_oneat_training_data_creator.ipynb
diff --git a/Notebooks/parasitic_training_data_creator.ipynb b/Notebooks/parasitic_training_data_creator.ipynb
@@ -73,15 +73,7 @@
    "metadata": {
     "scrolled": false
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "  4%|██▊                                                                           | 460/12489 [00:08<04:23, 45.71it/s]"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "for root, dirs, files in os.walk(data_folder):\n",
     "   if dirs!=[]:  \n",
@@ -93,18 +85,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "ba5f3a93",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(24998, 128, 128, 3) (24998, 2, 1)\n"
+     ]
+    }
+   ],
    "source": [
-    "MovieCreator.createNPZ(save_dir, axes = 'SXYC', save_name = npz_name, save_name_val = npz_val_name)"
+    "MovieCreator.createNPZ(save_dir, axes = 'SXYC', save_name = npz_name, save_name_val = npz_val_name, expand = False, flip_channel_axis = True)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9c968c4",
+   "id": "d2e1001d",
    "metadata": {},
    "outputs": [],
    "source": []

diff --git a/oneat/NEATUtils/MovieCreator.py b/oneat/NEATUtils/MovieCreator.py
@@ -792,7 +792,7 @@ def SegFreeImageLabelDataSet(image_dir, csv_dir,save_dir, static_name, static_la
                                                SegFreeImageMaker(t, y[key], x[key], image, crop_size, gridx, gridy, offset, total_categories, trainlabel, name + event_name + str(count), save_dir)    
                                                count = count + 1                 
 
-def createNPZ(save_dir, axes, save_name = 'Yolov0oneat', save_name_val = 'Yolov0oneatVal', static = False):
+def createNPZ(save_dir, axes, save_name = 'Yolov0oneat', save_name_val = 'Yolov0oneatVal', expand = True, static = False, flip_channel_axis = False):
 
             data = []
             label = []   
@@ -805,8 +805,9 @@ def createNPZ(save_dir, axes, save_name = 'Yolov0oneat', save_name_val = 'Yolov0
             names = [Readname(fname)  for fname in files_raw]
             #Normalize everything before it goes inside the training
             for i in range(0,len(NormalizeImages)):
-
+                   
                        n = NormalizeImages[i]
+
                        blankX = n
                        csvfname = save_dir + '/' + names[i] + '.csv'   
                        arr = [] 
@@ -816,19 +817,23 @@ def createNPZ(save_dir, axes, save_name = 'Yolov0oneat', save_name_val = 'Yolov0
                              arr = np.array(arr)
 
                        blankY = arr
-
                        blankY = np.expand_dims(blankY, -1)
-                       blankX = np.expand_dims(blankX, -1)
-
+                       if expand:
+
+                         blankX = np.expand_dims(blankX, -1)
+
                        data.append(blankX)
                        label.append(blankY)
 
 
 
             dataarr = np.asarray(data)
             labelarr = np.asarray(label)
+            if flip_channel_axis:
+                       np.swapaxes(dataarr, 1,-1)
             if static:
                 try:
+
                    dataarr = dataarr[:,0,:,:,:]
                 except:
 

diff --git a/oneat/NEATUtils/__pycache__/MovieCreator.cpython-39.pyc b/oneat/NEATUtils/__pycache__/MovieCreator.cpython-39.pyc
diff --git a/oneat/_version.py b/oneat/_version.py
@@ -0,0 +1 @@
+__version__= '2.7.8'
diff --git a/oneat/version.py b/oneat/version.py
@@ -1 +1 @@
-__version__= '2.7.7'
+__version__= '2.7.8'
diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 
 with open('README.md') as f:
     long_description = f.read()
-with open(path.join(_dir,'oneat','version.py'), encoding="utf-8") as f:
+with open(path.join(_dir,'oneat','_version.py'), encoding="utf-8") as f:
     exec(f.read())
 
 setup(