bugfix in water_mask + update to mintpy-v1.4.1-11 (#46)

+ water_mask: - bugfix since the water value read by mintpy from *.wbd file changed from -1 to 255 - update API usage to mintpy version 1.4.1-11 + closure_phase_bias:fix typo for the GitHub link + update to mintpy-v1.4.1-11 for the other notebooks
insarlab · Sep 23, 2022 · a3df6ce · a3df6ce
1 parent ce036bc
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diff --git a/applications/closure_phase_bias.ipynb b/applications/closure_phase_bias.ipynb
@@ -23,7 +23,7 @@
    "id": "d8b096a1",
    "metadata": {},
    "source": [
-    "In the following, we use the Barstow-Bristol Trough, CA dataset (as shown in Zheng et al., 2022) as an example to illustrate the use of `closure_phase_bias.py`. This dataset includes interferograms generated from 153 Sentinel-1 A/B SAR images at descending orbit 173 using [ISCE2](https://github.com/isceframework/isce2) [topsStack](https://github.com/isce-framework/isce2/tree/main/contrib/stack/topsStack) processor (Rosen et al., 2012; Fattahi et al., 2017) developed at JPL/Caltech. The stack of interferograms is freely available on Zenodo at: https://doi.org/10.5281/zenodo.6558341 (size: 13 GB).\n",
+    "In the following, we use the Barstow-Bristol Trough, CA dataset (as shown in Zheng et al., 2022) as an example to illustrate the use of `closure_phase_bias.py`. This dataset includes interferograms generated from 153 Sentinel-1 A/B SAR images at descending orbit 173 using [ISCE2](https://github.com/isce-framework/isce2) / [topsStack](https://github.com/isce-framework/isce2/tree/main/contrib/stack/topsStack) processor (Rosen et al., 2012; Fattahi et al., 2017) developed at JPL/Caltech. The stack of interferograms is freely available on Zenodo at: https://doi.org/10.5281/zenodo.6558341 (size: 13 GB).\n",
     "\n",
     "The average velocity maps of bw-1, bw-5, and bw-10 are shown in the figure below (right). Note that there are systematic descrepancies in these velocity maps. These descrepancies result from temporally inconsistent processes. We can use `closure_phase_bias.py` to estimate and remove these descrepancies.\n",
     "\n",
@@ -60,7 +60,6 @@
    "cell_type": "markdown",
    "id": "f2844294",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
    "source": [
@@ -84,7 +83,7 @@
    "source": [
     "%matplotlib inline\n",
     "import os\n",
-    "from mintpy import view\n",
+    "from mintpy.cli import view\n",
     "\n",
     "# define and go to the work directory\n",
     "work_dir = os.path.expanduser('~/data/DrylakeSenD173/mintpy')\n",
@@ -102,7 +101,6 @@
    "cell_type": "markdown",
    "id": "307a76f2",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
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@@ -214,7 +212,6 @@
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    "id": "e5b48e43",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
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@@ -416,7 +413,6 @@
    "cell_type": "markdown",
    "id": "a6690f43",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
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@@ -837,7 +833,6 @@
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    "metadata": {
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@@ -1565,7 +1560,6 @@
    "cell_type": "markdown",
    "id": "36125751",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
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diff --git a/applications/coherence_change_detection.ipynb b/applications/coherence_change_detection.ipynb
@@ -50,7 +50,6 @@
     "from skimage import exposure\n",
     "\n",
     "# mintpy modules\n",
-    "from mintpy import geocode, save_kmz\n",
     "from mintpy.objects import ifgramStack\n",
     "from mintpy.utils import readfile, writefile, utils as ut\n",
     "\n",
@@ -612,14 +611,13 @@
     "########################       GEOCODE RESULTS       ##################################\n",
     "#######################################################################################\n",
     "\n",
-    "geocode.main(f'cohChange_Fernandina-0917.h5 -l {geom_file}'.split())\n",
+    "!geocode.py cohChange_Fernandina-0917.h5 -l $geom_file\n",
     "\n",
     "#######################################################################################\n",
     "#####################       EXPORT RESULTS TO KMZ       ###############################\n",
     "#######################################################################################\n",
     "%matplotlib notebook\n",
-    "save_kmz.main('geo_cohChange_Fernandina-0917.h5 CCD_diff-092017 \\\n",
-    "              --cbar-label Eruption-Sep2017  -u CCD -c magma_r'.split())"
+    "!save_kmz.py geo_cohChange_Fernandina-0917.h5 CCD_diff-092017 --cbar-label Eruption-Sep2017 -u CCD -c magma_r"
    ]
   },
   {
@@ -662,7 +660,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.8.13"
   }
  },
  "nbformat": 4,

diff --git a/applications/plot_gps_quiver.ipynb b/applications/plot_gps_quiver.ipynb
@@ -26,11 +26,12 @@
     "import os\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "from mintpy.defaults.plot import *\n",
     "from mintpy.objects.gps import search_gps, GPS\n",
     "from mintpy.objects import sensor\n",
     "from mintpy.utils import utils as ut\n",
-    "from mintpy import view\n",
+    "from mintpy.view import prep_slice, plot_slice\n",
     "\n",
     "# input\n",
     "date12 = '20180706_20180712'\n",
@@ -140,7 +141,7 @@
     "cmd = 'view.py {} unwrapPhase-{} -m {} -d {} '.format(ifgram_file, date12, mask_file, geom_file)\n",
     "cmd += '--sub-lat -0.87 -0.77 --sub-lon -91.20 -91.08 '\n",
     "cmd += '--notitle -u cm -c jet_r --nocbar --lalo-label --lalo-max-num 3 --noverbose '\n",
-    "dv, atr, inps = view.prep_slice(cmd)\n",
+    "dv, atr, inps = prep_slice(cmd)\n",
     "print('Done.')"
    ]
   },
@@ -178,13 +179,13 @@
     "# Horizontal\n",
     "ax = axs[0]\n",
     "inps.lalo_loc = [1,0,0,1]\n",
-    "ax, inps, im = view.plot_slice(ax, dv, atr, inps)[0:3]\n",
+    "ax, inps, im = plot_slice(ax, dv, atr, inps)[0:3]\n",
     "q  = ax.quiver(gps_lons, gps_lats, dis_e, dis_n, zorder=10, units='width', pivot='tail')\n",
     "ax.quiverkey(q, X=0.1, Y=0.9, U=key_length, label='GPS horz = {:.0f} {}'.format(key_length, inps.disp_unit), labelpos='E', coordinates='figure')\n",
     "# Vertical\n",
     "ax = axs[1]\n",
     "inps.lalo_loc = [0,0,0,1]\n",
-    "ax, inps, im = view.plot_slice(ax, dv, atr, inps)[0:3]\n",
+    "ax, inps, im = plot_slice(ax, dv, atr, inps)[0:3]\n",
     "q  = ax.quiver(gps_lons, gps_lats, np.zeros(len(gps_lats)), dis_u, zorder=10, units='width', pivot='tail')\n",
     "ax.quiverkey(q, X=0.53, Y=0.9, U=key_length, label='GPS vert = {:.0f} {}'.format(key_length, inps.disp_unit), angle=90, labelpos='E', coordinates='figure')\n",
     "\n",
@@ -211,7 +212,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -225,9 +226,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.8.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/applications/stripmapApp_postProc.ipynb b/applications/stripmapApp_postProc.ipynb
@@ -35,9 +35,11 @@
     "import time\n",
     "from datetime import datetime as dt\n",
     "from decimal import Decimal\n",
+    "\n",
     "import h5py\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "from mintpy.utils import readfile, writefile, utils as ut\n",
     "\n",
     "work_dir = os.path.expanduser(\"~/insarlab/Others/Koae4shuangyu/\")\n",
@@ -111,9 +113,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -158,11 +158,13 @@
    "source": [
     "# geocoding\n",
     "for in_file, out_file in zip(in_files, out_files):\n",
-    "    cmd = \"geocode.py {f} -l {l} -b {b} -o {o} --lat-step -{s} --lon-step {s}\".format(f=in_file,\n",
-    "                                                                                      l=geom_file, \n",
-    "                                                                                      b=SNWE,\n",
-    "                                                                                      o=out_file,\n",
-    "                                                                                      s=step)\n",
+    "    cmd = \"geocode.py {f} -l {l} -b {b} -o {o} --lat-step -{s} --lon-step {s}\".format(\n",
+    "        f=in_file,\n",
+    "        l=geom_file, \n",
+    "        b=SNWE,\n",
+    "        o=out_file,\n",
+    "        s=step,\n",
+    "    )\n",
     "    print(cmd)\n",
     "    !{cmd}"
    ]
@@ -350,7 +352,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -364,9 +366,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.8.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/applications/tropo_gacos.ipynb b/applications/tropo_gacos.ipynb
@@ -27,9 +27,10 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "from skimage.transform import resize\n",
+    "\n",
     "from mintpy.objects import timeseries\n",
     "from mintpy.utils import ptime, readfile, utils as ut\n",
-    "from mintpy import view\n",
+    "from mintpy.cli import view\n",
     "\n",
     "# GACOS product directory\n",
     "ztd_dir = os.path.expanduser('~/insarlab/Kirishima/AlosAT424F620_630/GACOS')\n",
@@ -303,7 +304,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -317,7 +318,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.13"
   }
  },
  "nbformat": 4,

diff --git a/applications/water_mask.ipynb b/applications/water_mask.ipynb