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ornlneutronimaging · Jan 13, 2025 · 0b4a008 · 0b4a008
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diff --git a/documentation/source/tutorial_normalization_with_fewer_ob_than_sample.ipynb b/documentation/source/tutorial_normalization_with_fewer_ob_than_sample.ipynb
@@ -60,9 +60,7 @@
     "import os\n",
     "import sys\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -91,7 +89,6 @@
    "source": [
     "root_folder = os.path.dirname(os.getcwd())\n",
     "sys.path.append(root_folder)\n",
-    "import NeuNorm as neunorm\n",
     "from NeuNorm.normalization import Normalization\n",
     "from NeuNorm.roi import ROI"
    ]
@@ -132,7 +129,7 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample'\n",
+    "path_im = \"../data/sample\"\n",
     "assert os.path.exists(path_im)"
    ]
   },
@@ -159,9 +156,9 @@
    },
    "outputs": [],
    "source": [
-    "path_ob = '../data/ob/'\n",
-    "ob1 = path_ob + '0001.tif'\n",
-    "ob2 = path_ob + '0002.tif'\n",
+    "path_ob = \"../data/ob/\"\n",
+    "ob1 = path_ob + \"0001.tif\"\n",
+    "ob2 = path_ob + \"0002.tif\"\n",
     "assert os.path.exists(ob1)\n",
     "assert os.path.exists(ob2)"
    ]
@@ -191,7 +188,7 @@
    "source": [
     "o_norm = Normalization()\n",
     "o_norm.load(folder=path_im)\n",
-    "o_norm.load(file=[ob1, ob2], data_type='ob')"
+    "o_norm.load(file=[ob1, ob2], data_type=\"ob\")"
    ]
   },
   {
@@ -273,7 +270,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized_data = o_norm.data['normalized']"
+    "normalized_data = o_norm.data[\"normalized\"]"
    ]
   },
   {
@@ -338,7 +335,7 @@
     "roi_to_keep = ROI(x0=0, y0=0, width=2, height=2)\n",
     "o_norm.crop(roi=roi_to_keep)\n",
     "\n",
-    "norm_crop = o_norm.data['normalized']\n",
+    "norm_crop = o_norm.data[\"normalized\"]\n",
     "np.shape(norm_crop)"
    ]
   },

diff --git a/documentation/source/tutorial_using_array_input.ipynb b/documentation/source/tutorial_using_array_input.ipynb
@@ -62,11 +62,9 @@
     "import os\n",
     "import sys\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
     "import glob\n",
     "from PIL import Image\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -95,7 +93,6 @@
    "source": [
     "root_folder = os.path.dirname(os.getcwd())\n",
     "sys.path.append(root_folder)\n",
-    "import NeuNorm as neunorm\n",
     "from NeuNorm.normalization import Normalization\n",
     "from NeuNorm.roi import ROI"
    ]
@@ -136,8 +133,8 @@
    },
    "outputs": [],
    "source": [
-    "path_ob = os.path.abspath('../data/ob/')\n",
-    "list_open_beam = glob.glob(os.path.join(path_ob, '*.tif'))\n",
+    "path_ob = os.path.abspath(\"../data/ob/\")\n",
+    "list_open_beam = glob.glob(os.path.join(path_ob, \"*.tif\"))\n",
     "ob_data = []\n",
     "for _file in list_open_beam:\n",
     "    _ob_data = np.asarray(Image.open(_file))\n",
@@ -167,8 +164,8 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample'\n",
-    "list_sample = glob.glob(os.path.join(path_im, '*.tif'))\n",
+    "path_im = \"../data/sample\"\n",
+    "list_sample = glob.glob(os.path.join(path_im, \"*.tif\"))\n",
     "sample_data = []\n",
     "for _file in list_sample:\n",
     "    _sample_data = np.asarray(Image.open(_file))\n",
@@ -198,8 +195,8 @@
    },
    "outputs": [],
    "source": [
-    "path_df = '../data/df'\n",
-    "list_df = glob.glob(os.path.join(path_df, '*.tif'))\n",
+    "path_df = \"../data/df\"\n",
+    "list_df = glob.glob(os.path.join(path_df, \"*.tif\"))\n",
     "df_data = []\n",
     "for _file in list_df:\n",
     "    _df_data = np.asarray(Image.open(_file))\n",
@@ -231,8 +228,8 @@
    "source": [
     "o_norm = Normalization()\n",
     "o_norm.load(data=sample_data)\n",
-    "o_norm.load(data=ob_data, data_type='ob')\n",
-    "o_norm.load(data=df_data, data_type='df')"
+    "o_norm.load(data=ob_data, data_type=\"ob\")\n",
+    "o_norm.load(data=df_data, data_type=\"df\")"
    ]
   },
   {
@@ -340,7 +337,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized_data = o_norm.data['normalized']"
+    "normalized_data = o_norm.data[\"normalized\"]"
    ]
   },
   {
@@ -405,7 +402,7 @@
     "roi_to_keep = ROI(x0=0, y0=0, width=2, height=2)\n",
     "o_norm.crop(roi=roi_to_keep)\n",
     "\n",
-    "norm_crop = o_norm.data['normalized']\n",
+    "norm_crop = o_norm.data[\"normalized\"]\n",
     "np.shape(norm_crop)"
    ]
   },

diff --git a/documentation/source/tutorial_using_folder_input.ipynb b/documentation/source/tutorial_using_folder_input.ipynb
@@ -62,9 +62,7 @@
     "import os\n",
     "import sys\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -94,7 +92,6 @@
     "root_folder = os.path.dirname(os.getcwd())\n",
     "sys.path.append(root_folder)\n",
     "\n",
-    "import NeuNorm as neunorm\n",
     "from NeuNorm.normalization import Normalization\n",
     "from NeuNorm.roi import ROI"
    ]
@@ -135,7 +132,7 @@
    },
    "outputs": [],
    "source": [
-    "path_ob = '../data/ob/'\n",
+    "path_ob = \"../data/ob/\"\n",
     "assert os.path.exists(path_ob)"
    ]
   },
@@ -162,7 +159,7 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample'\n",
+    "path_im = \"../data/sample\"\n",
     "assert os.path.exists(path_im)"
    ]
   },
@@ -189,7 +186,7 @@
    },
    "outputs": [],
    "source": [
-    "path_df = '../data/df'\n",
+    "path_df = \"../data/df\"\n",
     "assert os.path.exists(path_df)"
    ]
   },
@@ -237,8 +234,8 @@
     }
    ],
    "source": [
-    "o_norm.load(folder=path_ob, data_type='ob', notebook=True)\n",
-    "o_norm.load(folder=path_df, data_type='df')"
+    "o_norm.load(folder=path_ob, data_type=\"ob\", notebook=True)\n",
+    "o_norm.load(folder=path_df, data_type=\"df\")"
    ]
   },
   {
@@ -351,7 +348,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized_data = o_norm.data['normalized']"
+    "normalized_data = o_norm.data[\"normalized\"]"
    ]
   },
   {
@@ -405,7 +402,7 @@
     "roi_to_keep = ROI(x0=0, y0=0, width=2, height=2)\n",
     "o_norm.crop(roi=roi_to_keep)\n",
     "\n",
-    "norm_crop = o_norm.data['normalized']\n",
+    "norm_crop = o_norm.data[\"normalized\"]\n",
     "np.shape(norm_crop)"
    ]
   },

diff --git a/notebooks/debugging_multi_roi_bug.ipynb b/notebooks/debugging_multi_roi_bug.ipynb
@@ -55,9 +55,7 @@
     "import os\n",
     "import sys\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -135,7 +133,7 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample'\n",
+    "path_im = \"../data/sample\"\n",
     "assert os.path.exists(path_im)"
    ]
   },
@@ -162,9 +160,9 @@
    },
    "outputs": [],
    "source": [
-    "path_ob = '../data/ob/'\n",
-    "ob1 = path_ob + '0001.tif'\n",
-    "ob2 = path_ob + '0002.tif'\n",
+    "path_ob = \"../data/ob/\"\n",
+    "ob1 = path_ob + \"0001.tif\"\n",
+    "ob2 = path_ob + \"0002.tif\"\n",
     "assert os.path.exists(ob1)\n",
     "assert os.path.exists(ob2)"
    ]
@@ -194,7 +192,7 @@
    "source": [
     "o_norm = Normalization()\n",
     "o_norm.load(folder=path_im)\n",
-    "o_norm.load(file=[ob1, ob2], data_type='ob')"
+    "o_norm.load(file=[ob1, ob2], data_type=\"ob\")"
    ]
   },
   {
@@ -238,7 +236,7 @@
    },
    "outputs": [],
    "source": [
-    "len(o_norm.data['sample']['data'])"
+    "len(o_norm.data[\"sample\"][\"data\"])"
    ]
   },
   {
@@ -268,7 +266,7 @@
    },
    "outputs": [],
    "source": [
-    "len(o_norm.data['sample']['data'])"
+    "len(o_norm.data[\"sample\"][\"data\"])"
    ]
   },
   {
@@ -294,7 +292,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized_data = o_norm.data['normalized']"
+    "normalized_data = o_norm.data[\"normalized\"]"
    ]
   },
   {
@@ -337,7 +335,7 @@
     "roi_to_keep = ROI(x0=0, y0=0, width=2, height=2)\n",
     "o_norm.crop(roi=roi_to_keep)\n",
     "\n",
-    "norm_crop = o_norm.data['normalized']\n",
+    "norm_crop = o_norm.data[\"normalized\"]\n",
     "np.shape(norm_crop)"
    ]
   },

diff --git a/notebooks/notebook_display_with_time_estimation.ipynb b/notebooks/notebook_display_with_time_estimation.ipynb
@@ -53,11 +53,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -85,11 +81,10 @@
    "outputs": [],
    "source": [
     "# root_folder = os.path.dirname(os.getcwd())\n",
-    "#sys.path.append(root_folder)\n",
-    "#sys.path.insert(0, os.path.abspath('..'))\n",
+    "# sys.path.append(root_folder)\n",
+    "# sys.path.insert(0, os.path.abspath('..'))\n",
     "import NeuNorm as neunorm\n",
-    "from NeuNorm.normalization import Normalization\n",
-    "from NeuNorm.roi import ROI"
+    "from NeuNorm.normalization import Normalization"
    ]
   },
   {
@@ -144,7 +139,7 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample'\n",
+    "path_im = \"../data/sample\"\n",
     "assert os.path.exists(path_im)"
    ]
   },

diff --git a/notebooks/testing_new_auto_gamma_filtering.ipynb b/notebooks/testing_new_auto_gamma_filtering.ipynb
@@ -54,10 +54,7 @@
    "source": [
     "import os\n",
     "import sys\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as patches\n",
-    "from matplotlib import gridspec\n",
+    "\n",
     "%matplotlib notebook"
    ]
   },
@@ -86,9 +83,7 @@
    "source": [
     "root_folder = os.path.dirname(os.getcwd())\n",
     "sys.path.insert(0, root_folder)\n",
-    "import NeuNorm as neunorm\n",
     "from NeuNorm.normalization import Normalization\n",
-    "from NeuNorm.roi import ROI\n",
     "import NeuNorm"
    ]
   },
@@ -142,7 +137,7 @@
    },
    "outputs": [],
    "source": [
-    "path_im = '../data/sample/'\n",
+    "path_im = \"../data/sample/\"\n",
     "assert os.path.exists(path_im)"
    ]
   },
@@ -196,7 +191,7 @@
    },
    "outputs": [],
    "source": [
-    "o_norm.export(file_type='tif', folder='/Users/j35/Desktop/tmp/', data_type='sample')"
+    "o_norm.export(file_type=\"tif\", folder=\"/Users/j35/Desktop/tmp/\", data_type=\"sample\")"
    ]
   },
   {