Update Notebooks
This commit is contained in:
parent
21f13dc864
commit
ae823b3a26
@ -4,7 +4,7 @@
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# GDAL vs Matplotlib\n",
|
||||
"# GDAL vs Matplotlib (vs OpenCV vs LibTIFF)\n",
|
||||
"\n",
|
||||
"We have in data fusion contest dataset TIFF file with 32 bit per sample. For now TRISKELE only work with less than 17 bps: `BOOST_ASSERT (bits < 17);`. I want to ensure that we can oppen such data with Python.\n"
|
||||
]
|
||||
@ -18,7 +18,10 @@
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"import gdal\n",
|
||||
"from pathlib import Path\n",
|
||||
"import subprocess"
|
||||
"import subprocess\n",
|
||||
"import numpy as np\n",
|
||||
"import pandas as pd\n",
|
||||
"import cv2"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -27,7 +30,8 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"file = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')"
|
||||
"file = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')\n",
|
||||
"ofile = Path('../Res/python_out.tif')"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -86,7 +90,6 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import numpy as np\n",
|
||||
"(np.power(2, (np.arange(4)[::-1] * 8)) * mat_data).sum(axis=2).shape"
|
||||
]
|
||||
},
|
||||
@ -127,13 +130,341 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.figure(figsize=(32,9))\n",
|
||||
"plt.imshow(raster * (raster < .25 * 1e38))\n",
|
||||
"raster.max()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"from ipywidgets import interact, interactive, fixed, interact_manual\n",
|
||||
"import ipywidgets as widgets\n",
|
||||
"\n",
|
||||
"def disp(x):\n",
|
||||
" display(x)\n",
|
||||
" plt.figure(figsize=(32,9))\n",
|
||||
" plt.imshow(raster * (raster < x))\n",
|
||||
" plt.colorbar()\n",
|
||||
" plt.show()\n",
|
||||
" plt.hist(raster.reshape(-1) * (raster.reshape(-1) < x), 100, log=True)\n",
|
||||
" plt.show()\n",
|
||||
" \n",
|
||||
"interact(disp, x=widgets.IntSlider(min=raster.min(),max=80,value=80));"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster_df = pd.DataFrame(raster.reshape(-1))\n",
|
||||
"raster_df.describe()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"rasterf = raster.copy()\n",
|
||||
"rasterf[rasterf == rasterf.max()] = 0"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"rasterf_df = pd.DataFrame(rasterf.reshape(-1))\n",
|
||||
"rasterf_df.describe()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(rasterf)\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()\n",
|
||||
"plt.hist(raster.reshape(-1) * (raster.reshape(-1) < .25 * 1e38), 100, log=True)\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Write TIFF file"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### OpenCV"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster_cv2 = cv2.imread(str(file), -1)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"(raster_cv2 != raster).sum()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"str(ofile)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ls ../Res"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"rasterf_im = np.expand_dims(rasterf, 2)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"cv2.imwrite(str(ofile), rasterf_im)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### GDAL"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"gdl_data.RasterXSize"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"cols = gdl_data.RasterXSize\n",
|
||||
"rows = gdl_data.RasterYSize\n",
|
||||
"\n",
|
||||
"format = 'GTiff'\n",
|
||||
"driver = gdal.GetDriverByName(format)\n",
|
||||
"dst_ds = driver.Create(str(ofile), cols, rows, 1, gdal.GDT_Byte)\n",
|
||||
"dst_ds.GetRasterBand(1).WriteArray(rasterf, 0, 0)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"dst_ds = None"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"#### Test "
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"!tiffinfo ../Res/python_out.tif"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(rasterf)\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"test_ofile = cv2.imread(str(ofile))\n",
|
||||
"display(test_ofile.shape)\n",
|
||||
"todf = pd.DataFrame(test_ofile.reshape(-1,3))\n",
|
||||
"display(todf.describe())\n",
|
||||
"plt.imshow(test_ofile[:,:,0])\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## LibTiff\n",
|
||||
"\n",
|
||||
"### Write"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import libtiff\n",
|
||||
"\n",
|
||||
"tiff = libtiff.TIFFimage(rasterf.astype(np.float16), description='test')\n",
|
||||
"tiff.write_file(ofile)#, compression='lzw')\n",
|
||||
"del tiff"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"!tiffinfo ../Res/python_out.tif"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ogdl_data = gdal.Open(str(ofile))\n",
|
||||
"ogdl_data.GetMetadata(), ogdl_data.RasterCount"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"otest = ogdl_data.GetRasterBand(1).ReadAsArray()\n",
|
||||
"otest.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(otest)\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"(otest != rasterf).sum()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Précision au millimètre :"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"np.isclose(otest, rasterf, rtol=1e-3).sum() / rasterf.size"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Read"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"tiff_r = libtiff.TIFF.open(file, mode='r')\n",
|
||||
"tiff_r.read_image().shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(tiff_r.read_image())\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"(tiff_r.read_image() != raster).sum()"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
|
||||
202
Notebooks/TIFF pour TRISKELE.ipynb
Normal file
202
Notebooks/TIFF pour TRISKELE.ipynb
Normal file
@ -0,0 +1,202 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"from pathlib import Path\n",
|
||||
"import numpy as np\n",
|
||||
"import libtiff"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## `float32` to `uint16`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Load raster"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"infile_path = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')\n",
|
||||
"outfile_path = Path('../Res/dem_u16.tif')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"infile = libtiff.TIFF.open(infile_path)\n",
|
||||
"raster = infile.read_image()\n",
|
||||
"raster.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(raster)\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Remove extremum"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster.max(), raster[raster != raster.max()].max()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster[raster == raster.max()] = raster[raster != raster.max()].max()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(raster)\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Scale to new representation"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"rep = np.iinfo(np.uint16)\n",
|
||||
"\n",
|
||||
"raster -= raster.min() - rep.min\n",
|
||||
"raster *= (rep.max - rep.min) / (raster.max() - raster.min())"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(raster)\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"np.iinfo(np.uint16).max, raster.max(), raster.astype(np.uint16).max()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Cast to new type"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster = raster.astype(np.uint16)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"plt.imshow(raster)\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Save raster"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"outfile = libtiff.TIFFimage(raster, description='TRISKELE raster')\n",
|
||||
"outfile.write_file(outfile_path)#, compression='lzw')\n",
|
||||
"outfile = None"
|
||||
]
|
||||
}
|
||||
],
|
||||
"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
|
||||
}
|
||||
@ -22,7 +22,8 @@
|
||||
"import subprocess\n",
|
||||
"import numpy as np\n",
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"import pandas as pd"
|
||||
"import pandas as pd\n",
|
||||
"import libtiff"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -55,7 +56,8 @@
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Files\n",
|
||||
"infile = Path('../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif')\n",
|
||||
"#infile = Path('../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif')\n",
|
||||
"infile = Path('../Res/dem_u16.tif')\n",
|
||||
"outfile = Path('../Res/out.tiff')\n",
|
||||
"\n",
|
||||
"area_conf = Path('../Res/area.txt')\n",
|
||||
@ -63,7 +65,7 @@
|
||||
"inertia_conf = Path('../Res/inertia.txt')\n",
|
||||
"\n",
|
||||
"# Attributes definition\n",
|
||||
"area = np.array([10,100,1000])\n",
|
||||
"area = np.arange(10) * 100 #* 10000#np.array([10,100,1000])\n",
|
||||
"deviation = np.array([10,100,1000])\n",
|
||||
"inertia = np.array([10,100,1000])\n",
|
||||
"np.savetxt(area_conf, area, fmt='%d')\n",
|
||||
@ -72,10 +74,10 @@
|
||||
"\n",
|
||||
"process = [triskele_bin.absolute(),\n",
|
||||
" '-i', infile.absolute(),\n",
|
||||
" '--tos-tree',\n",
|
||||
" '--max-tree',\n",
|
||||
" '--area', area_conf.absolute(),\n",
|
||||
" '--standard-deviation', deviation_conf.absolute(),\n",
|
||||
" '--moment-of-inertia', inertia_conf.absolute(),\n",
|
||||
" #'--standard-deviation', deviation_conf.absolute(),\n",
|
||||
" #'--moment-of-inertia', inertia_conf.absolute(),\n",
|
||||
" '-o', outfile.absolute()]\n",
|
||||
"\n",
|
||||
"display(' '.join(str(v) for v in process))\n",
|
||||
@ -90,8 +92,15 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"A = ' '\n",
|
||||
"A.join(str(v) for v in process)"
|
||||
"process = libtiff.TIFF.open(outfile)\n",
|
||||
"raster = process.read_image()\n",
|
||||
"raster.shape\n",
|
||||
"\n",
|
||||
"for chan in range(raster.shape[2]):\n",
|
||||
" plt.figure(figsize=(16,3))\n",
|
||||
" plt.imshow(raster[:,:,chan])\n",
|
||||
" plt.colorbar()\n",
|
||||
" plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -100,19 +109,22 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"out = plt.imread(outfile.absolute())\n",
|
||||
"display(out.shape)\n",
|
||||
"\n",
|
||||
"dwidth = 32\n",
|
||||
"plt.figure(figsize=(dwidth, dwidth * out.shape[0] / out.shape[1] * .80))\n",
|
||||
"#plt.figure(figsize=(16,9))\n",
|
||||
"\n",
|
||||
"display_channel = 2\n",
|
||||
"plt.imshow(out[:,:,display_channel] * (out[:,:,display_channel] < 50))\n",
|
||||
"rasterf = raster.astype(np.float)\n",
|
||||
"plt.figure(figsize=(16,3))\n",
|
||||
"plt.imshow(rasterf[:,:,0] - rasterf[:,:,-1])\n",
|
||||
"plt.colorbar()\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster[:,:,0] - raster[:,:,9]"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
|
||||
Loading…
Reference in New Issue
Block a user