Update Notebooks
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Notebooks/Attribute Profiles Classifier.ipynb
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252
Notebooks/Attribute Profiles Classifier.ipynb
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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import sys\n",
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"from pathlib import Path\n",
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"import numpy as np\n",
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"import libtiff\n",
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"import matplotlib.pyplot as plt\n",
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"\n",
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"triskele_path = Path('../triskele/python/')\n",
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"sys.path.append(str(triskele_path.resolve()))\n",
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"import triskele"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## List raster files"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"layers_files = [\n",
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" '../Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif',\n",
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" '../Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif',\n",
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" '../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif',\n",
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" '../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif',\n",
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" '../Data/phase1_rasters/Intensity_C1/UH17_GI1F051_TR.tif',\n",
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" '../Data/phase1_rasters/Intensity_C2/UH17_GI2F051_TR.tif',\n",
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" '../Data/phase1_rasters/Intensity_C3/UH17_GI3F051_TR.tif'\n",
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"]"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Define dataset dependent raster filtering"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"def DFC_filter(raster):\n",
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" ## Remove extrem values\n",
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" #raster[raster == raster.max()] = raster[raster != raster.max()].max()\n",
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" raster[raster > 1e4] = raster[raster < 1e4].max()\n",
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" #raster[raster == np.finfo(raster.dtype).max] = raster[raster != raster.max()].max()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Load rasters data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"layers = list()\n",
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"\n",
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"for file in layers_files:\n",
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" print('Loading {}'.format(file))\n",
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" layer = libtiff.TIFF.open(file).read_image()\n",
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" DFC_filter(layer)\n",
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" layers.append(layer)\n",
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"\n",
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"layers_stack = np.stack(layers, axis=2)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Display rasters"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"for i in range(layers_stack.shape[2]):\n",
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" plt.figure(figsize=(16*2,3*2))\n",
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" plt.imshow(layers_stack[:,:,i])\n",
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" plt.colorbar()\n",
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" plt.title(layers_files[i])\n",
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" plt.show()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Attributes filter with TRISKELE !"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"t = triskele.Triskele(layers_stack[0], verbose=False)\n",
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"attributes = t.filter()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"attributes.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"layers_stack.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"test = libtiff.TIFF.open('../Res/test.tif', mode='w')\n",
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"test.write_image(np.rollaxis(layers_stack, 2).astype(np.float32))\n",
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"test = None"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"layers_stack.shape[0]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"test = libtiff.TIFF.open('../Res/test.tif', mode='w')\n",
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"test.\n",
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"#test = None\n",
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"#test.write_tiles(layers_stack[:,:,0].astype(np.uint8), tile_width=layers_stack.shape[1], tile_height=layers_stack.shape[0])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"np.rollaxis(layers_stack, 2).shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"tiff = libtiff.TIFFimage(np.rollaxis(layers_stack, 1), description='BDQ')\n",
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"tiff.write_file('../Res/test.tif')\n",
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"del tiff"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"test = libtiff.TIFF.open('../Res/test.tif')\n",
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"for image in test.iter_images():\n",
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" print(image.shape)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"test = libtiff.TIFFimage(layers_stack)\n",
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"test.write_file('../Res/test.tif')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"for i in range(attributes.shape[2]):\n",
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" plt.figure(figsize=(16*2,3*2))\n",
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" plt.imshow(attributes[:,:,i])\n",
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" plt.colorbar()\n",
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" plt.title(layers_files[i])\n",
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" plt.show()"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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431
Notebooks/GDAL vs libtiff.ipynb
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431
Notebooks/GDAL vs libtiff.ipynb
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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import gdal\n",
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"from pathlib import Path\n",
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"import numpy as np"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"outfile = Path('../Res/test.tif')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"raster = np.arange(20 * 10).reshape(10, 20)\n",
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"raster.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"ds = gdal.Open(outfile.as_posix())\n",
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"ds"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"cols = raster.shape[1]\n",
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"rows = raster.shape[0]\n",
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"\n",
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"driver = gdal.GetDriverByName('GTiff')\n",
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"dst_ds = driver.Create(outfile.as_posix(), cols, rows, 2, gdal.GDT_Byte)\n",
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"dst_ds.GetRasterBand(1).WriteArray(raster.astype(np.uint8))\n",
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"dst_ds.GetRasterBand(2).WriteArray(raster.astype(np.uint8))\n",
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"dst_ds.FlushCache()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import gdal\n",
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"\n",
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"gdal.GDT_TypeCount"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"np_to_gdt = {\n",
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" np.uint8: gdal.GDT_Byte,\n",
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" np.float32: gdal.GDT_Float32,\n",
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" np.float64: gdal.GDT_Float64,\n",
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" np.uint16: gdal.GDT_Int16,\n",
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" np.uint32: gdal.GDT_Int32\n",
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" }\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"raster.dtype.type"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"np.double"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"np.savetxt?"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"raster.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"np.rollaxis(dst_ds.GetVirtualMemArray(), 0, 3)[:,:,0] == raster #[:] = np.repeat(raster, 2).reshape(2, rows, cols)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"gdl_data = gdal.Open('/tmp/outfile.tif')\n",
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"gdl_data.GetMetadata(), gdl_data.RasterCount"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"gdl_data.GetVirtualMemArray()[0,:,:] == gdl_data.GetRasterBand(1).ReadAsArray()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"gdl_data.GetRasterBand(1).ReadAsArray().shape, gdl_data.GetRasterBand(1).ReadAsArray().dtype"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import sys\n",
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"from pathlib import Path\n",
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"import numpy as np\n",
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"\n",
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"triskele_path = Path('../triskele/python/')\n",
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"sys.path.append(str(triskele_path.resolve()))\n",
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"import importlib\n",
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"import triskele\n",
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"\n",
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"importlib.reload(triskele)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"triskele.read('/tmp/outfile.tif')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"triskele.Triskele"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"gdl = gdal.Open('/tmp/outfile.tif')\n",
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"gdl.ReadAsArray()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import gdal\n",
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"\n",
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"def read(fname):\n",
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" gdl_data = gdal.Open(str(fname))\n",
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" #tmp = gdl_data.GetRasterBand(1).ReadAsArray()\n",
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" return gdl_data.ReadAsArray()\n",
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" #return np.rollaxis(gdl_data.GetVirtualMemArray(), 0, 3)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"qwe = gdal.Open('test.tif')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"qwe."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"read('/tmp/outfile.tif')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"X = np.arange(20*12*5).reshape(12,20,5)\n",
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"X.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"triskele.write('../Res/test.tif', X[:,:,0].astype(np.uint8))"
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]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"Y = triskele.read('../Res/test.tif')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"Y.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"(X.astype(np.uint8) == Y).all()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"len(X.shape)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"x = X[:,:,0]"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"x.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"np.expand_dims(X, 2).shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"triskele.write('test.tif', x)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"x.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"data = triskele.read('../Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"t = triskele.Triskele(data, verbose=True)\n",
|
||||
"res = t.filter(area=np.array([10,100,1000]))"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"data = np.stack((data, data), axis=2)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"data.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"res.shape, res.dtype"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"triskele.write('ttest.tif', res[:,:,0])"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"triskele.read('ttest.tif').shape"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 2
|
||||
}
|
||||
@ -9,13 +9,30 @@
|
||||
"import sys\n",
|
||||
"from pathlib import Path\n",
|
||||
"import numpy as np\n",
|
||||
"import libtiff\n",
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"\n",
|
||||
"triskele_path = Path('../triskele/python/')\n",
|
||||
"sys.path.append(str(triskele_path.resolve()))\n",
|
||||
"import triskele"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def DFC_filter(raster):\n",
|
||||
" raster[raster > 1e4] = raster[raster < 1e4].max()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## One raster"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
@ -23,8 +40,8 @@
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"infile = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')\n",
|
||||
"raster = libtiff.TIFF.open(infile).read_image()\n",
|
||||
"raster[raster == raster.max()] = raster[raster != raster.max()].max()"
|
||||
"raster = triskele.read(infile)\n",
|
||||
"DFC_filter(raster)"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -42,9 +59,11 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"area = np.array([10, 100, 1000])\n",
|
||||
"area = np.array([10, 100, 1e3, 1e4, 1e5])\n",
|
||||
"moi = np.array([.0, .01, .1, .2, .3, .4, .5, .9, .99, 1.])\n",
|
||||
"\n",
|
||||
"filtered = t.filter(tree='tos-tree', area=area)"
|
||||
"filtered = t.filter(tree='tos-tree')\n",
|
||||
"filtered.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -53,7 +72,81 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"filtered"
|
||||
"plt.figure(figsize=(16*1,5*1))\n",
|
||||
"plt.imshow(filtered[:,:].astype(np.float))\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## More raster"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"infile1 = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')\n",
|
||||
"infile2 = Path('../Data/phase1_rasters/Intensity_C1/UH17_GI1F051_TR.tif')\n",
|
||||
"raster1 = triskele.read(infile1)\n",
|
||||
"raster2 = triskele.read(infile2)\n",
|
||||
"DFC_filter(raster1)\n",
|
||||
"DFC_filter(raster2)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.figure(figsize=(16*1,5*1))\n",
|
||||
"plt.imshow(raster1[:,:].astype(np.float))\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()\n",
|
||||
"\n",
|
||||
"plt.figure(figsize=(16*1,5*1))\n",
|
||||
"plt.imshow(raster2[:,:].astype(np.float))\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"data = np.stack((raster1, raster2), axis=2)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"t = triskele.Triskele(data, verbose=False)\n",
|
||||
"f = t.filter(tree='tos-tree', area=area)\n",
|
||||
"f.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"for i in range(f.shape[2]):\n",
|
||||
" plt.figure(figsize=(16*1,5*1))\n",
|
||||
" plt.imshow(f[:,:,i].astype(np.float))\n",
|
||||
" plt.colorbar()\n",
|
||||
" plt.show()"
|
||||
]
|
||||
}
|
||||
],
|
||||
|
||||
Loading…
Reference in New Issue
Block a user