Merge pull request #15 from ngergihun/master

New reader and transform classes
Quasars · Sep 19, 2024 · 06b0450 · 06b0450
2 parents 660ff63 + bf03937
commit 06b0450
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diff --git a/pySNOM/__init__.py b/pySNOM/__init__.py
@@ -4,7 +4,7 @@
 Scanning Near-field Optical Microscopy (SNOM) analysis tools
 """
 from .defaults import defaults
-from .images import Image, Process
+from .images import Image, Transformation
 from .readers import Reader
 from .spectra import NeaSpectrum, NeaInterferogram
 # import images
@@ -14,4 +14,4 @@
 __version__ = '0.0.2'
 __author__ = 'Gergely Németh, Ferenc Borondics'
 __credits__ = 'Wigner Research Centre for Physics, Synchrotron SOLEIL'
-__all__ = ["defaults","Reader","Image","Process","NeaSpectrum","NeaInterferogram"]
+__all__ = ["defaults","Reader","Image","Transformation","NeaSpectrum","NeaInterferogram"]
diff --git a/pySNOM/examples/imageprocess.ipynb b/pySNOM/examples/imageprocess.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -24,59 +24,42 @@
    ],
    "source": [
     "import numpy as np\n",
-    "from pySNOM.readers import Reader\n",
-    "from pySNOM.images import Image, Data, DataTypes\n",
+    "import pySNOM\n",
+    "from pySNOM import readers\n",
+    "import os\n",
     "\n",
-    "filename = r'C:\\Users\\NEMETHG\\OneDrive\\Python\\pySNOM\\pySNOM\\datasets\\testPsHetData.gwy'\n",
+    "f = 'datasets/testPsHetData.gwy'\n",
+    "file_reader = readers.GwyReader(fullfilepath=os.path.join(pySNOM.__path__[0], f),channelname='O3A raw')\n",
+    "gwy_image = file_reader.read()\n",
     "\n",
-    "file_reader = Reader(filename)\n",
-    "# From raw data black\n",
-    "# Reads all the files\n",
-    "rawgwydata = file_reader.read_gwyfile()\n",
-    "measurement = Data(filename = filename, data = rawgwydata, mode = 'PsHet')\n",
-    "O3Aimage = measurement.getImageFromChannel('O3A raw')\n",
-    "\n",
-    "# From a single channel\n",
-    "channel_name = 'O3A raw'\n",
-    "O3Achanneldata = file_reader.read_gwychannel(channel_name)\n",
-    "O3Aimage = Image(O3Achanneldata)\n",
-    "O3Aimage.setChannel(channel_name)\n",
-    "print(f'Pixel 7-7: {O3Aimage.data[7][7]}')\n",
-    "print(f'Pixel 8-8: {O3Aimage.data[8][8]}')\n",
-    "print(f'Pixel 8-9: {O3Aimage.data[9][9]}')\n",
-    "\n",
-    "# Read the info file\n",
-    "info_filename = r'C:\\Users\\NEMETHG\\OneDrive\\Python\\pySNOM\\pySNOM\\datasets\\testinfofile.txt'\n",
-    "file_reader.setFilename(info_filename)\n",
-    "infodict = file_reader.read_nea_infofile()\n",
-    "# Set parameters from the info dictionary\n",
-    "O3Aimage.setParameters(infodict=infodict)"
+    "print(f'Pixel 7-7: {gwy_image.data[7][7]}')\n",
+    "print(f'Pixel 8-8: {gwy_image.data[8][8]}')\n",
+    "print(f'Pixel 8-9: {gwy_image.data[9][9]}')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " Measurement mode: MeasurementModes.PsHet\n",
-      " Channel: O2A raw\n",
-      " Data type: DataTypes.Amplitude\n",
-      " Demod order: 2\n",
-      "X resolution: 200\n",
-      "Data size: (200, 200)\n",
-      "PLT-EV-niceplace_spectrum_1665_cm-1\n"
+      "Pixel 7-7: 15.213262557983398\n",
+      "Pixel 8-8: 15.736936569213867\n",
+      "Pixel 8-9: 13.609171867370605\n"
      ]
     }
    ],
    "source": [
-    "print(f' Measurement mode: {O3Aimage.mode}\\n Channel: {O3Aimage.channel}\\n Data type: {O3Aimage.datatype}\\n Demod order: {O3Aimage.order}')\n",
-    "print(f'X resolution: {O3Aimage.xres}')\n",
-    "print(f'Data size: {np.shape(O3Aimage.data)}')\n",
-    "print(O3Aimage.parameters['Description'])"
+    "f = 'datasets/testPsHet O3A raw.gsf'\n",
+    "file_reader = readers.GsfReader(os.path.join(pySNOM.__path__[0], f))\n",
+    "gwy_image = file_reader.read()\n",
+    "\n",
+    "print(f'Pixel 7-7: {gwy_image.data[7][7]}')\n",
+    "print(f'Pixel 8-8: {gwy_image.data[8][8]}')\n",
+    "print(f'Pixel 8-9: {gwy_image.data[9][9]}')"
    ]
   },
   {
@@ -190,7 +173,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.0"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,