Added comments and fixed augmentation issue

carpenterlab · Jul 30, 2018 · 930e47e · 930e47e
1 parent f2d6a67
commit 930e47e
Show file tree

Hide file tree

Showing 4 changed files with 215 additions and 26 deletions.
diff --git a/examples/bbbc022_seg_config.py → examples/bbbc039_seg_config.py b/examples/bbbc022_seg_config.py → examples/bbbc039_seg_config.py
diff --git a/unet4nuclei/00-download-dataset.ipynb b/unet4nuclei/00-download-dataset.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,9 +14,16 @@
     "from config import config_vars"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Download zip files from BBBC website"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,63 +43,94 @@
     "assert metadata.ok"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Extract images"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
     "images_zip = os.path.join(config_vars['raw_images_dir'], 'images.zip')\n",
     "os.makedirs(config_vars['raw_images_dir'], exist_ok=True)\n",
     "with open(images_zip, 'wb') as f:\n",
     "    f.write(images.content)\n",
+    "    \n",
     "zip_ref = zipfile.ZipFile(images_zip, 'r')\n",
     "for file in zip_ref.namelist():\n",
     "    if file.startswith('images/'):\n",
     "        zip_ref.extract(file, config_vars['raw_images_dir'])\n",
+    "\n",
     "zip_ref.close()\n",
     "os.remove(images_zip)\n",
+    "\n",
     "for file in glob.glob(os.path.join(config_vars['raw_images_dir'], 'images/*')):\n",
     "    shutil.move(file, config_vars['raw_images_dir'])\n",
+    "\n",
     "shutil.rmtree(os.path.join(config_vars['raw_images_dir'], 'images'))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Extract annotations"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "masks_zip = os.path.join(config_vars['raw_annotations_dir'], 'masks.zip')\n",
     "os.makedirs(config_vars['raw_annotations_dir'], exist_ok=True)\n",
     "with open(masks_zip, 'wb') as f:\n",
     "    f.write(masks.content)\n",
+    "\n",
     "zip_ref = zipfile.ZipFile(masks_zip, 'r')\n",
     "for file in zip_ref.namelist():\n",
     "    if file.startswith('masks/'):\n",
     "        zip_ref.extract(file, config_vars['raw_annotations_dir'])\n",
+    "\n",
     "zip_ref.close()\n",
     "os.remove(masks_zip)\n",
+    "\n",
     "for file in glob.glob(os.path.join(config_vars['raw_annotations_dir'], 'masks/*')):\n",
     "    shutil.move(file, config_vars['raw_annotations_dir'])\n",
     "shutil.rmtree(os.path.join(config_vars['raw_annotations_dir'], 'masks'))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Extract metadata"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
     "metadata_zip = os.path.join(config_vars['root_directory'], 'metadata.zip')\n",
     "with open(metadata_zip, 'wb') as f:\n",
     "    f.write(metadata.content)\n",
+    "\n",
     "zip_ref = zipfile.ZipFile(metadata_zip, 'r')\n",
     "for file in zip_ref.namelist():\n",
     "    if file.startswith('metadata/'):\n",
     "        zip_ref.extract(file, config_vars['root_directory'])\n",
+    "\n",
     "zip_ref.close()\n",
     "os.remove(metadata_zip)\n",
+    "\n",
     "for file in glob.glob(os.path.join(config_vars['root_directory'], 'metadata/*')):\n",
     "    shutil.move(file, config_vars['root_directory'])\n",
     "shutil.rmtree(os.path.join(config_vars['root_directory'], 'metadata'))"

diff --git a/unet4nuclei/01-preprocessing.ipynb b/unet4nuclei/01-preprocessing.ipynb
diff --git a/unet4nuclei/utils/model_builder.py b/unet4nuclei/utils/model_builder.py
@@ -51,7 +51,7 @@ def get_core(dim1, dim2):
 
     d = keras.layers.UpSampling2D()(d)
 
-    y = keras.layers.merge([d, c], concat_axis=3, mode="concat")
+    y = keras.layers.merge.concatenate([d, c], axis=3)
 
     e = keras.layers.Convolution2D(256, 3, 3, **option_dict_conv)(y)
     e = keras.layers.BatchNormalization(**option_dict_bn)(e)
@@ -62,7 +62,7 @@ def get_core(dim1, dim2):
     e = keras.layers.UpSampling2D()(e)
 
 
-    y = keras.layers.merge([e, b], concat_axis=3, mode="concat")
+    y = keras.layers.merge.concatenate([e, b], axis=3)
 
     f = keras.layers.Convolution2D(128, 3, 3, **option_dict_conv)(y)
     f = keras.layers.BatchNormalization(**option_dict_bn)(f)
@@ -73,7 +73,7 @@ def get_core(dim1, dim2):
     f = keras.layers.UpSampling2D()(f)
 
 
-    y = keras.layers.merge([f, a], concat_axis=3, mode="concat")
+    y = keras.layers.merge.concatenate([f, a], axis=3)
 
     y = keras.layers.Convolution2D(64, 3, 3, **option_dict_conv)(y)
     y = keras.layers.BatchNormalization(**option_dict_bn)(y)
@@ -95,4 +95,4 @@ def get_model_3_class(dim1, dim2, activation="softmax"):
 
     model = keras.models.Model(x, y)
 
-    return model
+    return model