update notebooks for recent changes

Odek2 · Apr 2, 2019 · b4a28d9 · b4a28d9
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Showing 11 changed files with 114 additions and 86 deletions.
diff --git a/Alignment-RigRelatives.ipynb b/Alignment-RigRelatives.ipynb
@@ -35,32 +35,35 @@
    },
    "outputs": [],
    "source": [
-    "import os, glob, numpy as np\n",
-    "import micasense.capture\n",
+    "import os, glob\n",
+    "import micasense.capture as capture\n",
     "%matplotlib inline\n",
     "\n",
+    "panelNames = None\n",
     "\n",
+    "# This is an altum image with RigRelatives and a thermal band\n",
     "imagePath = os.path.join('.','data','ALTUM1SET','000')\n",
-    "panelPath = imagePath\n",
     "imageNames = glob.glob(os.path.join(imagePath,'IMG_0008_*.tif'))\n",
-    "panelNames = glob.glob(os.path.join(panelPath,'IMG_0000_*.tif'))\n",
+    "panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
     "\n",
-    "capture = micasense.capture.Capture.from_filelist(imageNames)\n",
-    "panelCap = micasense.capture.Capture.from_filelist(panelNames)\n",
-    "if panelCap.panels_in_all_expected_images():\n",
-    "    panel_irradiance = panelCap.panel_irradiance()\n",
+    "if panelNames is not None:\n",
+    "    panelCap = capture.Capture.from_filelist(panelNames)\n",
     "else:\n",
-    "    raise ValueError(\"Panels not detected in all images\")\n",
-    "\n",
-    "panelCap.plot_panels()\n",
+    "    panelCap = None\n",
     "\n",
-    "# Plotting the reflectance images in the capture will ensure that a reflectance image has been\n",
-    "# calculated for all images in the capture. In this case we use the dls irradiance during panel capture\n",
-    "# to calibrate to the panel, and then scale future dls_irradiance values using that factor\n",
+    "capture = capture.Capture.from_filelist(imageNames)\n",
     "\n",
-    "dls_factor = np.asarray(panel_irradiance) / np.asarray(panelCap.dls_irradiance()[0:5])\n",
-    "corrected_irradiance = capture.dls_irradiance()[0:5] * dls_factor\n",
-    "capture.plot_undistorted_reflectance(dls_factor)"
+    "if panelCap is not None:\n",
+    "    if panelCap.panel_albedo() is not None:\n",
+    "        panel_reflectance_by_band = panelCap.panel_albedo()\n",
+    "    else:\n",
+    "        panel_reflectance_by_band = [0.67, 0.69, 0.68, 0.61, 0.67] #RedEdge band_index order\n",
+    "    panel_irradiance = panelCap.panel_irradiance(panel_reflectance_by_band)    \n",
+    "    img_type = \"reflectance\"\n",
+    "    capture.plot_undistorted_reflectance(panel_irradiance)\n",
+    "else:\n",
+    "    img_type = \"radiance\"\n",
+    "    capture.plot_undistorted_radiance()"
    ]
   },
   {
@@ -88,7 +91,7 @@
     "\n",
     "warp_matrices = capture.get_warp_matrices()\n",
     "cropped_dimensions,edges = imageutils.find_crop_bounds(capture,warp_matrices)\n",
-    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, cv2.MOTION_HOMOGRAPHY, cropped_dimensions, None, img_type=\"reflectance\")\n",
+    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, cv2.MOTION_HOMOGRAPHY, cropped_dimensions, None, img_type=img_type)\n",
     "\n",
     "for i,mat in enumerate(warp_matrices):\n",
     "    print(\"Band {}:\\n{}\".format(i,mat))"
@@ -177,15 +180,14 @@
     "rows, cols, bands = im_display.shape\n",
     "driver = gdal.GetDriverByName('GTiff')\n",
     "outRaster = driver.Create(\"bgrnet.tiff\", cols, rows, 6, gdal.GDT_UInt16)\n",
-    "normalize = False\n",
+    "\n",
+    "normalize = panelCap is None\n",
     "\n",
     "# Output a 'stack' in the same band order as RedEdge/Alutm\n",
     "# Blue,Green,Red,NIR,RedEdge[,Thermal]\n",
     "\n",
     "# NOTE: NIR and RedEdge are not in wavelength order!\n",
     "\n",
-    "capture.compute_reflectance(panel_irradiance+[0])\n",
-    "\n",
     "for i in range(0,5):\n",
     "    outband = outRaster.GetRasterBand(i+1)\n",
     "    if normalize:\n",
@@ -254,19 +256,12 @@
     "ndvi = (im_aligned[:,:,3] - im_aligned[:,:,2]) / (im_aligned[:,:,3] + im_aligned[:,:,2])\n",
     "\n",
     "# remove shadowed areas (mask pixels with NIR reflectance < 20%))\n",
-    "ndvi[im_aligned[:,:,3] < 0.2] = 0 \n",
-    "\n",
-    "# plotutils.plotwithcolorbar(ndvi, \n",
-    "#                             figsize = (18,18), \n",
-    "#                             title = 'NDVI filtered to only plants over RGB base layer',\n",
-    "#                             vmin = 0,\n",
-    "#                             vmax = 1)\n",
-    "\n",
-    "\n",
+    "if img_type == 'reflectance':\n",
+    "    ndvi = np.ma.masked_where(im_aligned[:,:,3] < 0.20, ndvi)\n",
     "\n",
     "# Compute and display a histogram\n",
-    "hist_min = np.min(ndvi[np.where(np.logical_and(ndvi > 0, ndvi < 1))])\n",
-    "hist_max = np.max(ndvi[np.where(np.logical_and(ndvi > 0, ndvi < 1))])\n",
+    "hist_min = np.min(ndvi)\n",
+    "hist_max = np.max(ndvi)\n",
     "fig, axis = plt.subplots(1, 1, figsize=(10,4))\n",
     "axis.hist(ndvi.ravel(), bins=512, range=(hist_min, hist_max))\n",
     "plt.title(\"NDVI Histogram\")\n",
@@ -308,15 +303,15 @@
     "masked_ndre = np.ma.masked_where(ndvi < 0.45, ndre)\n",
     "\n",
     "# Compute a histogram\n",
-    "hist_min = np.min(masked_ndre[np.where(np.logical_and(masked_ndre > 0, masked_ndre < 1))])\n",
-    "hist_max = np.max(masked_ndre[np.where(np.logical_and(masked_ndre > 0, masked_ndre < 1))])\n",
+    "hist_min = np.min(masked_ndre)\n",
+    "hist_max = np.max(masked_ndre)\n",
     "fig, axis = plt.subplots(1, 1, figsize=(10,4))\n",
     "axis.hist(masked_ndre.ravel(), bins=512, range=(hist_min, hist_max))\n",
     "plt.title(\"NDRE Histogram (filtered to only plants)\")\n",
     "plt.show()\n",
     "\n",
-    "min_display_ndre = 0.2\n",
-    "max_display_ndre = 0.45\n",
+    "min_display_ndre = np.percentile(masked_ndre, 5)\n",
+    "max_display_ndre = np.percentile(masked_ndre, 99.5)\n",
     "\n",
     "fig, axis = plotutils.plot_overlay_withcolorbar(gamma_corr_rgb, \n",
     "                                    masked_ndre, \n",
@@ -375,9 +370,9 @@
     "                                        vmin=min_display_therm,vmax=max_display_therm,\n",
     "                                        overlay_alpha=0.25,\n",
     "                                        overlay_colormap='jet',\n",
-    "                                        overlay_steps=8,\n",
+    "                                        overlay_steps=16,\n",
     "                                        display_contours=True,\n",
-    "                                        contour_steps=8,\n",
+    "                                        contour_steps=16,\n",
     "                                        contour_alpha=.4,\n",
     "                                        contour_fmt=\"%.0fC\")\n",
     "    fig.savefig('thermal_over_rgb.png')"
@@ -408,7 +403,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},

diff --git a/Alignment.ipynb b/Alignment.ipynb
@@ -41,33 +41,47 @@
     "import micasense.capture as capture\n",
     "%matplotlib inline\n",
     "\n",
-    "## This is an older RedEdge image without RigRelatives\n",
-    "# imagePath = os.path.join(os.path.abspath('.'),'data','0000SET','000')\n",
-    "# imageNames = glob.glob(os.path.join(imagePath,'IMG_0001_*.tif'))\n",
-    "# panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
+    "panelNames = None\n",
+    "\n",
+    "# This is an older RedEdge image without RigRelatives\n",
+    "imagePath = os.path.join(os.path.abspath('.'),'data','0000SET','000')\n",
+    "imageNames = glob.glob(os.path.join(imagePath,'IMG_0001_*.tif'))\n",
+    "panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
+    "\n",
+    "# # Image from the example RedEdge imageSet (see the ImageSet notebook) without RigRelatives.\n",
+    "# imagePath = os.path.expanduser(os.path.join('~','Downloads','RedEdgeImageSet','0000SET'))\n",
+    "# imageNames = glob.glob(os.path.join(imagePath,'000','IMG_0013_*.tif'))\n",
+    "# panelNames = glob.glob(os.path.join(imagePath,'000','IMG_0000_*.tif'))\n",
     "\n",
     "# # This is an altum image with RigRelatives and a thermal band\n",
     "# imagePath = os.path.join('.','data','ALTUM1SET','000')\n",
     "# imageNames = glob.glob(os.path.join(imagePath,'IMG_0245_*.tif'))\n",
     "# panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
     "\n",
-    "# This is the example RedEdge imageSet without RigRelatives.\n",
-    "imagePath = os.path.expanduser(os.path.join('~','Downloads','RedEdgeImageSet','0000SET'))\n",
-    "imageNames = glob.glob(os.path.join(imagePath,'000','IMG_0013_*.tif'))\n",
-    "panelNames = glob.glob(os.path.join(imagePath,'000','IMG_0000_*.tif'))\n",
+    "# Allow this code to align both radiance and reflectance images; bu excluding\n",
+    "# a definition for panelNames above, radiance images will be used\n",
+    "# For panel images, efforts will be made to automatically extract the panel information\n",
+    "# but if the panel/firmware is before Altum 1.3.5, RedEdge 5.1.7 the panel reflectance\n",
+    "# will need to be set in the panel_reflectance_by_band variable.\n",
+    "# Note: radiance images will not be used to properly create NDVI/NDRE images below.\n",
+    "if panelNames is not None:\n",
+    "    panelCap = capture.Capture.from_filelist(panelNames)\n",
+    "else:\n",
+    "    panelCap = None\n",
     "\n",
-    "panelCap = capture.Capture.from_filelist(panelNames) \n",
     "capture = capture.Capture.from_filelist(imageNames)\n",
     "\n",
-    "if panelCap.panel_albedo() is not None:\n",
-    "    panel_reflectance_by_band = panelCap.panel_albedo()\n",
+    "if panelCap is not None:\n",
+    "    if panelCap.panel_albedo() is not None:\n",
+    "        panel_reflectance_by_band = panelCap.panel_albedo()\n",
+    "    else:\n",
+    "        panel_reflectance_by_band = [0.67, 0.69, 0.68, 0.61, 0.67] #RedEdge band_index order\n",
+    "    panel_irradiance = panelCap.panel_irradiance(panel_reflectance_by_band)    \n",
+    "    img_type = \"reflectance\"\n",
+    "    capture.plot_undistorted_reflectance(panel_irradiance)\n",
     "else:\n",
-    "    panel_reflectance_by_band = [0.67, 0.69, 0.68, 0.61, 0.67] #RedEdge band_index order\n",
-    "    \n",
-    "panel_irradiance = panelCap.panel_irradiance(panel_reflectance_by_band)\n",
-    "# Plotting the reflectance images in the capture will ensure that a reflectance image has been\n",
-    "# calculated for all images in the capture.\n",
-    "capture.plot_undistorted_reflectance(panel_irradiance)"
+    "    img_type = \"radiance\"\n",
+    "    capture.plot_undistorted_radiance()    "
    ]
   },
   {
@@ -166,7 +180,7 @@
     "rgb_band_indices = [2,1,0]\n",
     "cir_band_indices = [3,2,1]\n",
     "\n",
-    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, match_index, img_type=\"reflectance\")\n",
+    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, match_index, img_type=img_type)\n",
     "\n",
     "# Create a normalized stack for viewing\n",
     "im_display = np.zeros((im_aligned.shape[0],im_aligned.shape[1],im_aligned.shape[2]), dtype=np.float32 )\n",
@@ -221,7 +235,7 @@
     "# Apply a gamma correction to make the render appear closer to what our eyes would see\n",
     "gamma = 1.4\n",
     "gamma_corr_rgb = unsharp_rgb**(1.0/gamma)\n",
-    "fig = plt.figure(figsize=(18,18))\n",
+    "fig = plt.figure(figsize=(16,16))\n",
     "plt.imshow(gamma_corr_rgb, aspect='equal')\n",
     "plt.axis('off')\n",
     "plt.show()"
@@ -271,15 +285,13 @@
     "if im_aligned.shape[2] == 6:\n",
     "    filename = filename + \"t\" #thermal\n",
     "outRaster = driver.Create(filename+\".tiff\", cols, rows, 6, gdal.GDT_UInt16)\n",
-    "normalize = False\n",
+    "normalize = panelCap is None\n",
     "\n",
     "# Output a 'stack' in the same band order as RedEdge/Alutm\n",
     "# Blue,Green,Red,NIR,RedEdge[,Thermal]\n",
     "\n",
     "# NOTE: NIR and RedEdge are not in wavelength order!\n",
     "\n",
-    "capture.compute_reflectance(panel_irradiance+[0])\n",
-    "\n",
     "for i in range(0,5):\n",
     "    outband = outRaster.GetRasterBand(i+1)\n",
     "    if normalize:\n",
@@ -348,7 +360,8 @@
     "ndvi = (im_aligned[:,:,3] - im_aligned[:,:,2]) / (im_aligned[:,:,3] + im_aligned[:,:,2])\n",
     "\n",
     "# remove shadowed areas (mask pixels with NIR reflectance < 20%))\n",
-    "ndvi[im_aligned[:,:,3] < 0.2] = 0 \n",
+    "if img_type == 'reflectance':\n",
+    "    ndvi[im_aligned[:,:,3] < 0.2] = 0 \n",
     "\n",
     "# Compute and display a histogram\n",
     "hist_min = np.min(ndvi[np.where(np.logical_and(ndvi > 0, ndvi < 1))])\n",
@@ -534,7 +547,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},

diff --git a/Batch Processing.ipynb b/Batch Processing.ipynb
@@ -41,8 +41,8 @@
     "import os, glob\n",
     "import multiprocessing\n",
     "\n",
-    "images_dir = os.path.expanduser(os.path.join('~','Downloads','RedEdgeImageSet','0000SET'))\n",
-    "panelNames = glob.glob(os.path.join(images_dir,'000','IMG_0000_*.tif'))\n",
+    "imagePath = os.path.expanduser(os.path.join('~','Documents','MicaSense','Micashare','sets','2019-02-26-Lettuce','raw'))\n",
+    "panelNames = glob.glob(os.path.join(imagePath,'0004SET','000','IMG_0000_*.tif'))\n",
     "panelCap = micasense.capture.Capture.from_filelist(panelNames)\n",
     "\n",
     "# Make sure to update or replace this if using your own data.\n",
@@ -69,7 +69,7 @@
     "def update_f(val):\n",
     "    f.value=val\n",
     "\n",
-    "%time imgset = imageset.ImageSet.from_directory(images_dir, progress_callback=update_f)\n",
+    "%time imgset = imageset.ImageSet.from_directory(imagePath, progress_callback=update_f)\n",
     "update_f(1.0)"
    ]
   },
@@ -95,17 +95,19 @@
     "from numpy import float32\n",
     "\n",
     "# Use the warp_matrices derived from the Alignment Tutorial for this RedEdge set without RigRelatives\n",
-    "warp_matrices = [array([[ 1.0022864e+00, -2.5218742e-03, -7.8897724e+00],\n",
-    "       [ 2.3614613e-03,  1.0036647e+00, -1.3134360e+01],\n",
-    "       [-1.7785960e-06,  1.1342933e-06,  1.0000000e+00]], dtype=float32), array([[1., 0., 0.],\n",
+    "warp_matrices = [array([[ 1.0040672e+00, -4.0104943e-03, -9.5216265e+00],\n",
+    "       [ 2.2561555e-03,  1.0027155e+00,  4.2039639e+01],\n",
+    "       [ 5.0572447e-07, -2.1989829e-06,  1.0000000e+00]], dtype=float32), array([[1., 0., 0.],\n",
     "       [0., 1., 0.],\n",
-    "       [0., 0., 1.]], dtype=float32), array([[ 9.9724644e-01, -1.5535479e-03,  1.2301332e+00],\n",
-    "       [ 8.6746749e-04,  9.9738181e-01, -1.6499146e+00],\n",
-    "       [-8.2814904e-07, -3.4492047e-07,  1.0000000e+00]], dtype=float32), array([[ 1.0007139e+00, -8.4427306e-03,  1.6312788e+01],\n",
-    "       [ 6.2834658e-03,  9.9977130e-01, -1.6011746e+00],\n",
-    "       [-1.9520005e-06, -6.3761996e-07,  1.0000000e+00]], dtype=float32), array([[ 9.9284184e-01,  9.2153507e-04,  1.6069824e+01],\n",
-    "       [-3.2895375e-03,  9.9262553e-01, -5.0334185e-01],\n",
-    "       [-1.5845230e-06, -1.7681158e-06,  1.0000000e+00]], dtype=float32)]"
+    "       [0., 0., 1.]], dtype=float32), array([[ 9.9754542e-01, -4.7137290e-03, -1.1499515e-02],\n",
+    "       [ 4.0390319e-03,  9.9641830e-01,  3.2048538e+01],\n",
+    "       [ 8.6146406e-07, -9.0479244e-07,  1.0000000e+00]], dtype=float32), array([[ 9.9953163e-01, -9.4728440e-04, -5.5923462e+00],\n",
+    "       [ 3.1482654e-05,  1.0024158e+00,  4.9206558e+01],\n",
+    "       [-1.0887084e-06,  1.2995536e-06,  1.0000000e+00]], dtype=float32), array([[ 1.0025666e+00, -2.9827280e-03, -9.4002628e+00],\n",
+    "       [ 3.3366329e-03,  1.0009472e+00,  1.4802245e+01],\n",
+    "       [ 1.5620793e-06, -8.3874954e-07,  1.0000000e+00]], dtype=float32), array([[ 6.35209892e-02,  1.17877689e-05,  1.40322785e+01],\n",
+    "        [-4.56733969e-04,  6.35520044e-02,  1.15592432e+01],\n",
+    "        [-4.15804231e-06, -2.63551964e-06,  1.00000000e+00]])]"
    ]
   },
   {
@@ -144,7 +146,7 @@
     "    outputFilename = capture.uuid+'.tif'\n",
     "    fullOutputPath = os.path.join(outputPath, outputFilename)\n",
     "    if (not os.path.exists(fullOutputPath)) or overwrite:\n",
-    "        capture.save_capture_as_reflectance_stack(fullOutputPath, irradiance_list=irradiance, warp_matrices=warp_matrices)\n",
+    "        capture.save_capture_as_stack(fullOutputPath, irradiance_list=irradiance, warp_matrices=warp_matrices)\n",
     "    capture.clear_image_data()\n",
     "    update_f2(float(i)/float(len(imgset.captures)))\n",
     "update_f2(1.0)\n",
@@ -259,7 +261,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   }
  },
  "nbformat": 4,

diff --git a/Captures.ipynb b/Captures.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Captures\n",
+    "A `micasense.capture.Capture` object holds a set of 5 (or in the case of Altum 6) images which are captured at the same moment together in a MicaSense camera.  Files which meet this criteria will tend to have the same filename except for the suffix, but that is not required to load a captures.  Captures can be loaded by starting with one image by calling Capture.from_file('file_name.tif') and adding others using the append_file, or by providing a list of filenames or images.  See capture.py for more creation methods."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -62,7 +70,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},

diff --git a/ImageSets.ipynb b/ImageSets.ipynb
@@ -13,6 +13,16 @@
     "## Load a directory of images into an ImageSet"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -232,7 +242,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},

diff --git a/Images.ipynb b/Images.ipynb
@@ -91,7 +91,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},

diff --git a/MicaSense Image Processing Setup.ipynb b/MicaSense Image Processing Setup.ipynb
@@ -237,7 +237,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.1"
   },
   "toc": {
    "nav_menu": {},