TRISKELE can not read 32 bps TIFF 😭

Notebooks/GDAL vs Matplotlib.ipynb

@@ -0,0 +1,159 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# GDAL vs Matplotlib\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"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import gdal\n",
+    "from pathlib import Path\n",
+    "import subprocess"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "file = Path('../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "info = subprocess.Popen(['tiffinfo', file], stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n",
+    "print(info.communicate()[0].decode())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mat_data = plt.imread(file)\n",
+    "mat_data.shape, mat_data.dtype"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gdl_data = gdal.Open(str(file))\n",
+    "gdl_data.GetMetadata(), gdl_data.RasterCount"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gdl_data.GetRasterBand(1).ReadAsArray().shape, gdl_data.GetRasterBand(1).ReadAsArray().dtype"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## There.\n",
+    "\n",
+    "`matplotlib` is derping around with bps. \n",
+    "\n",
+    "Maybe each byte is split `[a, b, c, d]` as $V = a 2^{24} + b 2^{16} + c 2^8 + d$"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "(np.power(2, (np.arange(4)[::-1] * 8)) * mat_data).sum(axis=2).shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "raster = gdl_data.GetRasterBand(1).ReadAsArray()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.figure(figsize=(32,9))\n",
+    "plt.imshow(raster)\n",
+    "plt.colorbar()\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.hist(raster.reshape(-1), 100, log=True)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.figure(figsize=(32,9))\n",
+    "plt.imshow(raster * (raster < .25 * 1e38))\n",
+    "plt.colorbar()\n",
+    "plt.show()\n",
+    "plt.hist(raster.reshape(-1) * (raster.reshape(-1) < .25 * 1e38), 100, log=True)\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "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
+}

Notebooks/TRYSKELE Wrapper.ipynb

@@ -48,16 +48,6 @@
     "print('STDOUT:\\n' + tryskele.stdout.read().decode() + '\\nSTDERR:\\n' + tryskele.stderr.read().decode())"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "area = np.array([42,100,1000])\n",
-    "np.savetxt(area_conf, area)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -73,7 +63,7 @@
     "inertia_conf   = Path('../Res/inertia.txt')\n",
     "\n",
     "# Attributes definition\n",
-    "area      = np.arange(100)#np.array([10,100,1000])\n",
+    "area      = 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",
@@ -88,8 +78,10 @@
     "           '--moment-of-inertia', inertia_conf.absolute(),\n",
     "           '-o', outfile.absolute()]\n",
     "\n",
+    "display(' '.join(str(v) for v in process))\n",
+    "\n",
     "tryskele = subprocess.Popen(process, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n",
-    "print('STDOUT:\\n' + tryskele.stdout.read().decode() + '\\nSTDERR:\\n' + tryskele.stderr.read().decode())"
+    "print('Return code: ' + str(tryskele.returncode) + '\\nSTDOUT:\\n' + tryskele.stdout.read().decode() + '\\nSTDERR:\\n' + tryskele.stderr.read().decode())"
    ]
   },
   {
@@ -98,7 +90,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "np.expand_dims(out[:,:,0] < 50, axis=2).shape"
+    "A = ' '\n",
+    "A.join(str(v) for v in process)"
    ]
   },
   {

deps.txt

@@ -0,0 +1 @@
+python-pillow