Add support for Panchro camera serie

Author: Sebastien Courroux

.gitignore

@@ -1,8 +1,6 @@
 # Add any directories, files, or patterns you don't want to be tracked by version control
 *.pyc
 .ipynb_checkpoints
-.vscode
-/.idea
 __pycache__
 /dist/
 /*.egg-info

Alignment v2.ipynb

@@ -39,9 +39,9 @@
     "panelNames = None\n",
     "paneCap = None\n",
     "\n",
-    "imagePath = os.path.join('.','data','10BANDSET','000')\n",
-    "imageNames = glob.glob(os.path.join(imagePath,'IMG_0431_*.tif'))\n",
-    "panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
+    "imagePath = os.path.join('.','data','REDEDGE-MX-DUAL')\n",
+    "imageNames = glob.glob(os.path.join(imagePath,'IMG_0007_*.tif'))\n",
+    "panelNames = glob.glob(os.path.join(imagePath,'IMG_0001_*.tif'))\n",
     "\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",
@@ -115,7 +115,7 @@
     "warp_mode = cv2.MOTION_HOMOGRAPHY # MOTION_HOMOGRAPHY or MOTION_AFFINE. For Altum images only use HOMOGRAPHY\n",
     "pyramid_levels = 3 # for 10-band imagery we use a 3-level pyramid. In some cases\n",
     "\n",
-    "print(\"Alinging images. Depending on settings this can take from a few seconds to many minutes\")\n",
+    "print(\"Aligning images. Depending on settings this can take from a few seconds to many minutes\")\n",
     "# Can potentially increase max_iterations for better results, but longer runtimes\n",
     "warp_matrices, alignment_pairs = imageutils.align_capture(capture,\n",
     "                                                          ref_index = match_index,\n",
@@ -137,11 +137,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [],
    "source": [
+    "\n",
     "cropped_dimensions, edges = imageutils.find_crop_bounds(capture, warp_matrices, warp_mode=warp_mode)\n",
-    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, match_index, img_type=img_type)"
+    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, match_index, img_type=img_type)\n",
+    "display(im_aligned)\n",
+    "print(\"fff\")\n",
+    "im_aligned = capture.create_aligned_capture(warp_matrices=warp_matrices, motion_type=warp_mode, img_type=img_type, match_index=match_index)\n",
+    "display(im_aligned)"
    ]
   },
   {
@@ -269,7 +276,7 @@
     "\n",
     "sort_by_wavelength = True # set to false if you want stacks in camera-band-index order\n",
     "    \n",
-    "outRaster = driver.Create(filename+\".tiff\", cols, rows, bands, gdal.GDT_UInt16, options = [ 'INTERLEAVE=BAND','COMPRESS=DEFLATE' ])\n",
+    "outRaster = driver.Create(filename+\"C.tiff\", cols, rows, bands, gdal.GDT_UInt16, options = [ 'INTERLEAVE=BAND','COMPRESS=DEFLATE' ])\n",
     "try:\n",
     "    if outRaster is None:\n",
     "        raise IOError(\"could not load gdal GeoTiff driver\")\n",
@@ -481,7 +488,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -495,7 +502,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.12"
   },
   "toc": {
    "nav_menu": {},

Alignment-10Band.ipynb

@@ -38,13 +38,20 @@
     "import os, glob\n",
     "import micasense.capture as capture\n",
     "%matplotlib inline\n",
+    "from pathlib import Path\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",
-    "imageNames = glob.glob(os.path.join(imagePath,'IMG_0008_*.tif'))\n",
-    "panelNames = glob.glob(os.path.join(imagePath,'IMG_0000_*.tif'))\n",
+    "# This is an Altum image with RigRelatives and a thermal band\n",
+    "\n",
+    "imagePath = Path(\"./data/ALTUM\")\n",
+    "\n",
+    "# these will return lists of image paths as strings \n",
+    "imageNames = list(imagePath.glob('IMG_0021_*.tif'))\n",
+    "imageNames = [x.as_posix() for x in imageNames]\n",
+    "\n",
+    "panelNames = list(imagePath.glob('IMG_0000_*.tif'))\n",
+    "panelNames = [x.as_posix() for x in panelNames]\n",
     "\n",
     "if panelNames is not None:\n",
     "    panelCap = capture.Capture.from_filelist(panelNames)\n",
@@ -61,7 +68,7 @@
     "    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_reflectance_by_band = [0.49, 0.49, 0.49, 0.49, 0.49] #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",
@@ -97,11 +104,14 @@
     "import micasense.imageutils as imageutils\n",
     "import micasense.plotutils as plotutils\n",
     "\n",
+    "reference_band = 5\n",
     "warp_mode = cv2.MOTION_HOMOGRAPHY\n",
-    "warp_matrices = capture.get_warp_matrices()\n",
+    "warp_matrices = capture.get_warp_matrices(ref_index=reference_band)\n",
+    "\n",
+    "cropped_dimensions,edges = imageutils.find_crop_bounds(capture,warp_matrices,reference_band=reference_band)\n",
+    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, reference_band, img_type=img_type)\n",
     "\n",
-    "cropped_dimensions,edges = imageutils.find_crop_bounds(capture,warp_matrices)\n",
-    "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, None, img_type=img_type)\n",
+    "print(im_aligned.shape)\n",
     "\n",
     "print(\"warp_matrices={}\".format(warp_matrices))"
    ]
@@ -128,7 +138,7 @@
     "cir_band_indices = [3,2,1]\n",
     "\n",
     "# Create an empty normalized stack for viewing\n",
-    "im_display = np.zeros((im_aligned.shape[0],im_aligned.shape[1],capture.num_bands+1), dtype=np.float32 )\n",
+    "im_display = np.zeros((im_aligned.shape[0],im_aligned.shape[1],im_aligned.shape[2]), dtype=np.float32 )\n",
     "\n",
     "im_min = np.percentile(im_aligned[:,:,0:2].flatten(),  0.1)  # modify with these percentilse to adjust contrast\n",
     "im_max = np.percentile(im_aligned[:,:,0:2].flatten(), 99.9)  # for many images, 0.5 and 99.5 are good values\n",
@@ -451,7 +461,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -465,7 +475,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.12"
   },
   "toc": {
    "nav_menu": {},

Alignment-RigRelatives.ipynb

@@ -34,30 +34,28 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [],
    "source": [
     "import os, glob\n",
     "import micasense.capture as capture\n",
     "%matplotlib inline\n",
+    "from pathlib import Path\n",
+    "import matplotlib.pyplot as plt\n",
+    "plt.rcParams[\"figure.facecolor\"] = \"w\"\n",
     "\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",
+    "imagePath = Path(\"./data/ALTUM\")\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",
+    "# these will return lists of image paths as strings \n",
+    "imageNames = list(imagePath.glob('IMG_0021_*.tif'))\n",
+    "imageNames = [x.as_posix() for x in imageNames]\n",
     "\n",
+    "panelNames = list(imagePath.glob('IMG_0000_*.tif'))\n",
+    "panelNames = [x.as_posix() for x in panelNames]\n",
     "\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",
@@ -76,7 +74,7 @@
     "    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_reflectance_by_band = [0.49, 0.49, 0.49, 0.49, 0.49] #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",
@@ -130,7 +128,7 @@
     "warp_mode = cv2.MOTION_HOMOGRAPHY # MOTION_HOMOGRAPHY or MOTION_AFFINE. For Altum images only use HOMOGRAPHY\n",
     "pyramid_levels = 0 # for images with RigRelatives, setting this to 0 or 1 may improve alignment\n",
     "\n",
-    "print(\"Alinging images. Depending on settings this can take from a few seconds to many minutes\")\n",
+    "print(\"Aligning images. Depending on settings this can take from a few seconds to many minutes\")\n",
     "# Can potentially increase max_iterations for better results, but longer runtimes\n",
     "warp_matrices, alignment_pairs = imageutils.align_capture(capture,\n",
     "                                                          ref_index = match_index,\n",
@@ -155,7 +153,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cropped_dimensions, edges = imageutils.find_crop_bounds(capture, warp_matrices, warp_mode=warp_mode)\n",
+    "cropped_dimensions, edges = imageutils.find_crop_bounds(capture, warp_matrices, warp_mode=warp_mode, reference_band=match_index)\n",
+    "print(cropped_dimensions)\n",
     "im_aligned = imageutils.aligned_capture(capture, warp_matrices, warp_mode, cropped_dimensions, match_index, img_type=img_type)"
    ]
   },
@@ -288,7 +287,7 @@
     "\n",
     "if im_aligned.shape[2] == 6:\n",
     "    filename = filename + \"t\" #thermal\n",
-    "outRaster = driver.Create(filename+\".tiff\", cols, rows, im_aligned.shape[2], gdal.GDT_UInt16)\n",
+    "outRaster = driver.Create(filename+\"B.tiff\", cols, rows, im_aligned.shape[2], gdal.GDT_UInt16)\n",
     "\n",
     "normalize = (img_type == 'radiance') # normalize radiance images to fit with in UInt16\n",
     "\n",
@@ -559,7 +558,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -573,7 +572,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.12"
   },
   "toc": {
    "nav_menu": {},