topsApp_asf.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "7ebeb130-b055-45c4-9ea3-470e2e7371b9",
   "metadata": {},
   "source": [
    "# Interferogram Processing with ISCE topsApp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "d28f5cc8-07fe-4495-a2ae-2129c2e65781",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Import required packages\n",
    "import logging\n",
    "log = logging.getLogger()\n",
    "log.setLevel(logging.WARN)\n",
    "import os\n",
    "import getpass\n",
    "import asf_search as asf\n",
    "import isce\n",
    "from os import listdir\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from osgeo import gdal\n",
    "import matplotlib.pyplot as plt\n",
    "from datetime import datetime, timedelta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "5999c18a-f543-4ce1-bb76-f3ff30caac85",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/jovyan/.local/ARIA-tools/tools/bin:/home/jovyan/.local/ARIA-tools/tools/ARIAtools:/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications:/home/jovyan/.local/envs/insar_analysis/bin:/opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/bin:/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/bin:/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications\n"
     ]
    }
   ],
   "source": [
    "# Set environment variables so that you can call ISCE from the command line\n",
    "os.environ['ISCE_HOME'] = os.path.dirname(isce.__file__)\n",
    "os.environ['ISCE_ROOT'] = os.path.dirname(os.environ['ISCE_HOME'])\n",
    "os.environ['PATH']+='{ISCE_HOME}/bin:{ISCE_HOME}/applications'.format(**os.environ)\n",
    "print(os.environ['PATH'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "62ee8ac5-2b33-4ef1-b714-9d8122ff25ee",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications/topsApp.py\n"
     ]
    }
   ],
   "source": [
    "!which topsApp.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f0146d52-8fe5-4a90-97b1-758bd3cc1dbd",
   "metadata": {},
   "outputs": [],
   "source": [
    "def plotcomplexdata(GDALfilename,\n",
    "                    title=None, aspect=1,\n",
    "                    datamin=None, datamax=None,\n",
    "                    interpolation='nearest',\n",
    "                    draw_colorbar=None, colorbar_orientation=\"horizontal\"):\n",
    "    # Load the data into numpy array\n",
    "    ds = gdal.Open(GDALfilename, gdal.GA_ReadOnly)\n",
    "    slc = ds.GetRasterBand(1).ReadAsArray()\n",
    "    transform = ds.GetGeoTransform()\n",
    "    ds = None\n",
    "    \n",
    "    # getting the min max of the axes\n",
    "    firstx = transform[0]\n",
    "    firsty = transform[3]\n",
    "    deltay = transform[5]\n",
    "    deltax = transform[1]\n",
    "    lastx = firstx+slc.shape[1]*deltax\n",
    "    lasty = firsty+slc.shape[0]*deltay\n",
    "    ymin = np.min([lasty,firsty])\n",
    "    ymax = np.max([lasty,firsty])\n",
    "    xmin = np.min([lastx,firstx])\n",
    "    xmax = np.max([lastx,firstx])\n",
    "\n",
    "    # put all zero values to nan and do not plot nan\n",
    "    try:\n",
    "        slc[slc==0]=np.nan\n",
    "    except:\n",
    "        pass\n",
    "    \n",
    "    fig = plt.figure(figsize=(18, 16))\n",
    "    ax = fig.add_subplot(1,2,1)\n",
    "    cax1=ax.imshow(np.abs(slc), vmin = datamin, vmax=datamax,\n",
    "                   cmap='gray', extent=[xmin,xmax,ymin,ymax],\n",
    "                   interpolation=interpolation)\n",
    "    ax.set_title(title + \" (amplitude)\")\n",
    "    if draw_colorbar is not None:\n",
    "        cbar1 = fig.colorbar(cax1,orientation=colorbar_orientation)\n",
    "    ax.set_aspect(aspect)\n",
    "\n",
    "    ax = fig.add_subplot(1,2,2)\n",
    "    cax2 =ax.imshow(np.angle(slc), cmap='rainbow',\n",
    "                    vmin=-np.pi, vmax=np.pi,\n",
    "                    extent=[xmin,xmax,ymin,ymax],\n",
    "                    interpolation=interpolation)\n",
    "    ax.set_title(title + \" (phase [rad])\")\n",
    "    if draw_colorbar is not None:\n",
    "        cbar2 = fig.colorbar(cax2, orientation=colorbar_orientation)\n",
    "    ax.set_aspect(aspect)\n",
    "    plt.show()\n",
    "    \n",
    "    # clearing the data\n",
    "    slc = None\n",
    "    \n",
    "def plotdata(GDALfilename, band=1,\n",
    "             title=None,colormap='gray',\n",
    "             aspect=1, background=None,\n",
    "             datamin=None, datamax=None,\n",
    "             interpolation='nearest',\n",
    "             nodata = None,\n",
    "             draw_colorbar=True, colorbar_orientation=\"horizontal\"):\n",
    "    \n",
    "    # Read the data into an array\n",
    "    ds = gdal.Open(GDALfilename, gdal.GA_ReadOnly)\n",
    "    data = ds.GetRasterBand(band).ReadAsArray()\n",
    "    transform = ds.GetGeoTransform()\n",
    "    ds = None\n",
    "    \n",
    "    try:\n",
    "        if nodata is not None:\n",
    "            data[data == nodata] = np.nan\n",
    "    except:\n",
    "        pass\n",
    "        \n",
    "    # getting the min max of the axes\n",
    "    firstx = transform[0]\n",
    "    firsty = transform[3]\n",
    "    deltay = transform[5]\n",
    "    deltax = transform[1]\n",
    "    lastx = firstx+data.shape[1]*deltax\n",
    "    lasty = firsty+data.shape[0]*deltay\n",
    "    ymin = np.min([lasty,firsty])\n",
    "    ymax = np.max([lasty,firsty])\n",
    "    xmin = np.min([lastx,firstx])\n",
    "    xmax = np.max([lastx,firstx])\n",
    "\n",
    "    # put all zero values to nan and do not plot nan\n",
    "    if background is None:\n",
    "        try:\n",
    "            data[data==0]=np.nan\n",
    "        except:\n",
    "            pass\n",
    "        \n",
    "        fig = plt.figure(figsize=(18, 16))\n",
    "    ax = fig.add_subplot(111)\n",
    "    cax = ax.imshow(data, vmin = datamin, vmax=datamax,\n",
    "                    cmap=colormap, extent=[xmin,xmax,ymin,ymax],\n",
    "                    interpolation=interpolation)\n",
    "    ax.set_title(title)\n",
    "    if draw_colorbar is not None:\n",
    "        cbar = fig.colorbar(cax,orientation=colorbar_orientation)\n",
    "    ax.set_aspect(aspect)    \n",
    "    plt.show()\n",
    "    \n",
    "    # clearing the data\n",
    "    data = None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "4060e60d-7795-47b3-98ce-381390c85542",
   "metadata": {},
   "outputs": [],
   "source": [
    "# make required directories\n",
    "dirs = ['/home/jovyan/rmnp_landslide/proc/orbital', '/home/jovyan/rmnp_landslide/proc/SLC']\n",
    "for i in dirs:\n",
    "    if not os.path.exists(i):\n",
    "        os.makedirs(i)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d09a4451-ccc7-42ad-ba41-b12b52adf82f",
   "metadata": {},
   "source": [
    "## Define desired pairs from list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "378c7a1c-7a82-48ab-811f-316ba5637dcd",
   "metadata": {},
   "outputs": [],
   "source": [
    "scene_list = ['S1B_IW_SLC__1SDV_20200717T005351_20200717T005418_022504_02AB6A_333A',\n",
    "              'S1B_IW_SLC__1SDV_20200717T005351_20200717T005418_022504_02AB6A_333A',\n",
    "              'S1B_IW_SLC__1SDV_20200722T010143_20200722T010210_022577_02AD97_0AF9',\n",
    "              'S1B_IW_SLC__1SDV_20200722T010208_20200722T010235_022577_02AD97_AE1D',\n",
    "              'S1B_IW_SLC__1SDV_20200729T005352_20200729T005419_022679_02B0C0_8427',\n",
    "              'S1B_IW_SLC__1SDV_20200803T010144_20200803T010211_022752_02B2E3_2F86',\n",
    "              'S1B_IW_SLC__1SDV_20200803T010209_20200803T010236_022752_02B2E3_C178',\n",
    "              'S1B_IW_SLC__1SDV_20200810T005352_20200810T005419_022854_02B621_D8F8',\n",
    "              'S1B_IW_SLC__1SDV_20200815T010145_20200815T010212_022927_02B84B_AD30',\n",
    "              'S1B_IW_SLC__1SDV_20200815T010210_20200815T010237_022927_02B84B_FCB6',\n",
    "              'S1B_IW_SLC__1SDV_20200822T005353_20200822T005420_023029_02BB99_67C5',\n",
    "              'S1B_IW_SLC__1SDV_20200827T010146_20200827T010213_023102_02BDCC_5F7D',\n",
    "              'S1B_IW_SLC__1SDV_20200827T010211_20200827T010238_023102_02BDCC_BB77',\n",
    "              'S1B_IW_SLC__1SDV_20200903T005354_20200903T005421_023204_02C10B_ABD8',\n",
    "              'S1B_IW_SLC__1SDV_20200908T010146_20200908T010213_023277_02C345_9DE5',\n",
    "              'S1B_IW_SLC__1SDV_20200908T010211_20200908T010238_023277_02C345_0255'\n",
    "             ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "67728df9-8452-4582-927f-d18ea37c8ab9",
   "metadata": {},
   "outputs": [],
   "source": [
    "def select_pairs(scene_list, max_temp_bline):\n",
    "    scene_dates = {}\n",
    "    for scene in scene_list:\n",
    "        date = scene[17:25]\n",
    "        scene_dates[date] = scene\n",
    "        \n",
    "    int_dict = {}\n",
    "    for date1 in scene_dates:\n",
    "        for date2 in scene_dates:\n",
    "            if datetime.strptime(date2, '%Y%m%d')-datetime.strptime(date1, '%Y%m%d') < timedelta(days=max_temp_bline) and not date1 >= date2 :\n",
    "                int_dict[f'{date1}-{date2}'] = [scene_dates[date1], scene_dates[date2]]\n",
    "    \n",
    "    return int_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "ab510c4c-b46f-47d9-9fd4-615e5e801505",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'20200717-20200722': ['S1B_IW_SLC__1SDV_20200717T005351_20200717T005418_022504_02AB6A_333A',\n",
       "  'S1B_IW_SLC__1SDV_20200722T010208_20200722T010235_022577_02AD97_AE1D'],\n",
       " '20200722-20200729': ['S1B_IW_SLC__1SDV_20200722T010208_20200722T010235_022577_02AD97_AE1D',\n",
       "  'S1B_IW_SLC__1SDV_20200729T005352_20200729T005419_022679_02B0C0_8427'],\n",
       " '20200729-20200803': ['S1B_IW_SLC__1SDV_20200729T005352_20200729T005419_022679_02B0C0_8427',\n",
       "  'S1B_IW_SLC__1SDV_20200803T010209_20200803T010236_022752_02B2E3_C178'],\n",
       " '20200803-20200810': ['S1B_IW_SLC__1SDV_20200803T010209_20200803T010236_022752_02B2E3_C178',\n",
       "  'S1B_IW_SLC__1SDV_20200810T005352_20200810T005419_022854_02B621_D8F8'],\n",
       " '20200810-20200815': ['S1B_IW_SLC__1SDV_20200810T005352_20200810T005419_022854_02B621_D8F8',\n",
       "  'S1B_IW_SLC__1SDV_20200815T010210_20200815T010237_022927_02B84B_FCB6'],\n",
       " '20200815-20200822': ['S1B_IW_SLC__1SDV_20200815T010210_20200815T010237_022927_02B84B_FCB6',\n",
       "  'S1B_IW_SLC__1SDV_20200822T005353_20200822T005420_023029_02BB99_67C5'],\n",
       " '20200822-20200827': ['S1B_IW_SLC__1SDV_20200822T005353_20200822T005420_023029_02BB99_67C5',\n",
       "  'S1B_IW_SLC__1SDV_20200827T010211_20200827T010238_023102_02BDCC_BB77'],\n",
       " '20200827-20200903': ['S1B_IW_SLC__1SDV_20200827T010211_20200827T010238_023102_02BDCC_BB77',\n",
       "  'S1B_IW_SLC__1SDV_20200903T005354_20200903T005421_023204_02C10B_ABD8'],\n",
       " '20200903-20200908': ['S1B_IW_SLC__1SDV_20200903T005354_20200903T005421_023204_02C10B_ABD8',\n",
       "  'S1B_IW_SLC__1SDV_20200908T010211_20200908T010238_023277_02C345_0255']}"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "select_pairs(scene_list, 12)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2e05fd89-b225-4e64-9454-82dbad158776",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Download SLCs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9df661c4-5c7c-4dc3-afd8-20d06976eecf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      " ········\n"
     ]
    }
   ],
   "source": [
    "EARTHDATA_LOGIN = \"qbrencherUW\"\n",
    "EARTHDATA_PASSWORD = getpass.getpass()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "20aa6ff2-b63f-4b3c-a458-074b1013c250",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Change to SLC directory \n",
    "os.chdir('/home/jovyan/rmnp_landslide/proc/SLC')\n",
    "\n",
    "logging.getLogger(\"urllib3\").setLevel(logging.WARNING)\n",
    "\n",
    "reference = 'S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A'\n",
    "secondary = 'S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591'\n",
    "granules = [reference, secondary]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "b6cf8414-927c-400d-875b-6eab2510ddf4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 57.7 ms, sys: 20.6 ms, total: 78.4 ms\n",
      "Wall time: 2min 7s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "results = asf.granule_search(granules)\n",
    "session = asf.ASFSession().auth_with_creds(EARTHDATA_LOGIN, EARTHDATA_PASSWORD)\n",
    "results.download(path='/home/jovyan/rmnp_landslide/proc/SLC', processes=2, session=session)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "c5876980-2230-47d5-9e43-3b4795a19f83",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591', 'S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A']\n"
     ]
    }
   ],
   "source": [
    "# Create a list of zipped SLCs. Assume there are no other files with .zip extension in SLC directory\n",
    "datadir = listdir('/home/jovyan/rmnp_landslide/proc/SLC')\n",
    "\n",
    "scenes = []\n",
    "for file in datadir:\n",
    "    if file[-4:]=='.zip':\n",
    "        scenes.append(file[:-4])\n",
    "        \n",
    "print(scenes)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bf8418d5-1c62-45fc-a043-72dc81b3ee57",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Get orbital files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "5a82516b-1b93-420a-9aeb-c9052db93c66",
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir('/home/jovyan/rmnp_landslide/proc/orbital')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "f1f24305-d4ef-4aa3-b926-e8fb4fb502fb",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "--2022-09-06 16:22:01--  https://raw.githubusercontent.com/isce-framework/isce2/main/contrib/stack/topsStack/fetchOrbit.py\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 5054 (4.9K) [text/plain]\n",
      "Saving to: ‘fetchOrbit.py’\n",
      "\n",
      "     0K ....                                                  100% 71.1M=0s\n",
      "\n",
      "2022-09-06 16:22:01 (71.1 MB/s) - ‘fetchOrbit.py’ saved [5054/5054]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "wget -nc https://raw.githubusercontent.com/isce-framework/isce2/main/contrib/stack/topsStack/fetchOrbit.py\n",
    "chmod +x fetchOrbit.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "482a97f5-856f-4c29-9138-4d72ac5573e6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reference time:  2021-09-03 01:02:44\n",
      "Satellite name:  S1B\n",
      "Downloading URL:  https://scihub.copernicus.eu/gnss/odata/v1/Products('a9d9a788-1ad4-4f2d-8fee-be5f33d9be15')/$value\n",
      "Reference time:  2021-08-22 01:02:43\n",
      "Satellite name:  S1B\n",
      "Downloading URL:  https://scihub.copernicus.eu/gnss/odata/v1/Products('009b4375-2957-42ff-afcc-ff7682ffc4ed')/$value\n"
     ]
    }
   ],
   "source": [
    "# grab orbital files with fetchOrbit.py\n",
    "for file in scenes:\n",
    "    os.system(f'./fetchOrbit.py -i {file}')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "87a2aaa3-583f-4616-824a-6f76f1c33194",
   "metadata": {},
   "source": [
    "## Write input file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "080d91d9-93bc-4a5c-b828-2b17adb37250",
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir('/home/jovyan/rmnp_landslide/proc/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "57348913-cc16-4f81-9ead-fd86ae9d224a",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('topsApp.xml', 'w') as f:\n",
    "    f.write(f\"\"\"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
    "<topsApp>\n",
    "  <component name=\"topsinsar\">\n",
    "    <property name=\"Sensor name\">SENTINEL1</property>\n",
    "    <component name=\"reference\">\n",
    "        <property name=\"orbit directory\">/home/jovyan/rmnp_landslide/proc/orbital</property>\n",
    "        <property name=\"output directory\">reference</property>\n",
    "        <property name=\"safe\">/home/jovyan/rmnp_landslide/proc/SLC/{reference}.zip</property>\n",
    "    </component>\n",
    "    <component name=\"secondary\">\n",
    "        <property name=\"orbit directory\">/home/jovyan/rmnp_landslide/proc/orbital</property>\n",
    "        <property name=\"output directory\">secondary</property>\n",
    "        <property name=\"safe\">/home/jovyan/rmnp_landslide/proc/SLC/{secondary}.zip</property>\n",
    "    </component>\n",
    "    <property name=\"demfilename\">/home/jovyan/rmnp_landslide/proc/usgs_10m.dem.wgs84</property>\n",
    "    <property name=\"useGPU\">True</property>\n",
    "    <property name=\"swaths\">[3]</property>\n",
    "    <property name=\"range looks\">6</property>\n",
    "    <property name=\"azimuth looks\">1</property>\n",
    "    <property name=\"region of interest\">[40.295, 40.310, -105.69, -105.67]</property>\n",
    "    <property name=\"do esd\">False</property>\n",
    "    <property name=\"do ionospherecorrection\">False</property>\n",
    "    <property name=\"do unwrap\">True</property>\n",
    "    <property name=\"unwrapper name\">snaphu_mcf</property>\n",
    "    <property name=\"do denseoffsets\">False</property>\n",
    "    <property name=\"geocode demfilename\">/home/jovyan/rmnp_landslide/proc/usgs_10m.dem.wgs84</property>\n",
    "    <property name=\"geocode list\">['merged/topophase.cor', 'merged/filt_topophase.unw', 'merged/filt_topophase.flat']</property>\n",
    "  </component>\n",
    "</topsApp>\"\"\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6a13d46c-f042-4ba3-94c5-ab18f527dad4",
   "metadata": {},
   "source": [
    "## topsApp processing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "3772c46e-033a-4363-80ac-6a1cbde2ad71",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "2022-09-06 16:22:19,738 - isce.insar - INFO - ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "Step processing\n",
      "Cannot open PICKLE/startup\n",
      "Running step preprocess\n",
      "Input XML files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.zip/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.SAFE/annotation/s1b-iw3-slc-vv-20210822t010216-20210822t010241-028352-036202-006.xml']\n",
      "Input TIFF files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.zip/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.SAFE/measurement/s1b-iw3-slc-vv-20210822t010216-20210822t010241-028352-036202-006.tiff']\n",
      "Manifest files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.zip/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.SAFE/manifest.safe']\n",
      "MANS:  /home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.zip S1B_IW_SLC__1SDV_20210822T010216_20210822T010243_028352_036202_417A.SAFE/manifest.safe\n",
      "Setting IPF version to :  003.31\n",
      "Extracting orbit from Orbit File:  /home/jovyan/rmnp_landslide/proc/orbital/S1B_OPER_AUX_POEORB_OPOD_20210911T112002_V20210821T225942_20210823T005942.EOF\n",
      "Number of Bursts before cropping:  9\n",
      "Number of Bursts after cropping:  1\n",
      "Updating burst number from 1 to 1\n",
      "Input XML files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.zip/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.SAFE/annotation/s1b-iw3-slc-vv-20210903t010217-20210903t010242-028527-036777-006.xml']\n",
      "Input TIFF files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.zip/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.SAFE/measurement/s1b-iw3-slc-vv-20210903t010217-20210903t010242-028527-036777-006.tiff']\n",
      "Manifest files:  ['/vsizip//home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.zip/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.SAFE/manifest.safe']\n",
      "MANS:  /home/jovyan/rmnp_landslide/proc/SLC/S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.zip S1B_IW_SLC__1SDV_20210903T010217_20210903T010244_028527_036777_F591.SAFE/manifest.safe\n",
      "Setting IPF version to :  003.31\n",
      "Extracting orbit from Orbit File:  /home/jovyan/rmnp_landslide/proc/orbital/S1B_OPER_AUX_POEORB_OPOD_20210923T111947_V20210902T225942_20210904T005942.EOF\n",
      "Number of Bursts before cropping:  9\n",
      "Number of Bursts after cropping:  1\n",
      "Updating burst number from 1 to 1\n",
      "2022-09-06 16:22:41,823 - isce.topsinsar.runPreprocessor - INFO - \n",
      "####################################################################################################\n",
      "    runPreprocessor\n",
      "----------------------------------------------------------------------------------------------------\n",
      "common.Input list of swaths to process:  = [3]\n",
      "reference.burstLength_3 = 1517\n",
      "reference.burstWidth_3 = 25688\n",
      "reference.numberOfBursts_3 = 1\n",
      "reference.sensor.ascendingnodetime = 2021-08-22 00:51:25.751642\n",
      "reference.sensor.family = topsswathslc\n",
      "reference.sensor.folder = None\n",
      "reference.sensor.imagingmode = TOPS\n",
      "reference.sensor.mission = S1B\n",
      "reference.sensor.name = topsswathslc_name\n",
      "reference.sensor.numberofbursts = 1\n",
      "reference.sensor.processingfacility = Airbus Defence and Space-Toulouse, France\n",
      "reference.sensor.processingsoftwareversion = 003.31\n",
      "reference.sensor.processingsystem = Sentinel-1 IPF\n",
      "reference.sensor.spacecraftname = Sentinel-1\n",
      "secondary.burstLength_3 = 1517\n",
      "secondary.burstWidth_3 = 25688\n",
      "secondary.numberOfBursts_3 = 1\n",
      "secondary.sensor.ascendingnodetime = 2021-09-03 00:51:26.275161\n",
      "secondary.sensor.family = topsswathslc\n",
      "secondary.sensor.folder = None\n",
      "secondary.sensor.imagingmode = TOPS\n",
      "secondary.sensor.mission = S1B\n",
      "secondary.sensor.name = topsswathslc_name\n",
      "secondary.sensor.numberofbursts = 1\n",
      "secondary.sensor.processingfacility = Airbus Defence and Space-Toulouse, France\n",
      "secondary.sensor.processingsoftwareversion = 003.31\n",
      "secondary.sensor.processingsystem = Sentinel-1 IPF\n",
      "secondary.sensor.spacecraftname = Sentinel-1\n",
      "####################################################################################################\n",
      "Dumping the application's pickle object _insar to file  PICKLE/preprocess\n",
      "The remaining steps are (in order):  ['computeBaselines', 'verifyDEM', 'topo', 'subsetoverlaps', 'coarseoffsets', 'coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step computeBaselines\n",
      "Estimated burst offset:  0\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "No swaths contain any burst overlaps ... cannot continue for interferometry applications\n",
      "2022-09-06 16:22:42,016 - isce.topsinsar.runPreprocessor - INFO - \n",
      "####################################################################################################\n",
      "    runComputeBaseline\n",
      "----------------------------------------------------------------------------------------------------\n",
      "baseline.IW-3 Bpar at midrange for first common burst = -81.90186355030949\n",
      "baseline.IW-3 Bpar at midrange for last common burst = -81.90186355030949\n",
      "baseline.IW-3 Bperp at midrange for first common burst = 91.11931282362576\n",
      "baseline.IW-3 Bperp at midrange for last common burst = 91.11931282362576\n",
      "baseline.IW-3 First common burst in reference = 0\n",
      "baseline.IW-3 First common burst in secondary = 0\n",
      "baseline.IW-3 Last common burst in reference = 1\n",
      "baseline.IW-3 Last common burst in secondary = 1\n",
      "baseline.IW-3 Number of bursts in reference = 1\n",
      "baseline.IW-3 Number of bursts in secondary = 1\n",
      "baseline.IW-3 Number of common bursts = 1\n",
      "####################################################################################################\n",
      "Dumping the application's pickle object _insar to file  PICKLE/computeBaselines\n",
      "The remaining steps are (in order):  ['verifyDEM', 'topo', 'subsetoverlaps', 'coarseoffsets', 'coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step verifyDEM\n",
      "Writing geotrans to VRT for usgs_10m.dem.wgs84\n",
      "Dumping the application's pickle object _insar to file  PICKLE/verifyDEM\n",
      "The remaining steps are (in order):  ['topo', 'subsetoverlaps', 'coarseoffsets', 'coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "CPU times: user 303 ms, sys: 101 ms, total: 404 ms\n",
      "Wall time: 22.9 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "!topsApp.py --start=preprocess --end=verifyDEM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "f9734643-1f0f-4154-8eae-7ac6ee103985",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "2022-09-06 16:22:42,663 - isce.insar - INFO - ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "Step processing\n",
      "Running step topo\n",
      "2022-09-06 16:22:42,774 - isce.zerodop.topozero - WARNING - Default Peg heading set to: -0.23633792544467572\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 0 - by - 1 \n",
      "901706\t2.32956\t\n",
      "GDAL open (R): usgs_10m.dem.wgs84.vrt\n",
      "API open (WR): geom_reference/IW3/lat_01.rdr\n",
      "API open (WR): geom_reference/IW3/lon_01.rdr\n",
      "API open (WR): geom_reference/IW3/hgt_01.rdr\n",
      "API open (WR): geom_reference/IW3/los_01.rdr\n",
      "C pointer already created. Finalize and recreate if image dimensions changed.\n",
      "C pointer already created. Finalize and recreate if image dimensions changed.\n",
      " Initializing biquintic interpolator\n",
      " Orbit interpolation method: hermite\n",
      " Max threads used:            8\n",
      " DEM parameters:\n",
      " Dimensions:        10812       10812\n",
      " Top Left:   -106.00100000000000        41.000599999999999     \n",
      " Spacing:    9.2592599999999998E-005  -9.2592599999999998E-005\n",
      " Lon:   -106.00100000000000       -104.99998140140001     \n",
      " Lat:    39.999581401400000        41.000599999999999     \n",
      "  \n",
      " Estimated DEM bounds needed for global height range: \n",
      " Lon:   -106.17159515748293       -104.72074806954606     \n",
      " Lat:    40.102200168631065        40.727269807507113     \n",
      " Warning: west limit may be insufficient for global height range\n",
      " Warning: east limit may be insufficient for global height range\n",
      "  \n",
      " Actual DEM bounds used: \n",
      " Dimensions:        10812        6753\n",
      " Top Left:   -106.00100000000000        40.727359237400002     \n",
      " Spacing:    9.2592599999999998E-005  -9.2592599999999998E-005\n",
      " Lon:   -106.00100000000000       -104.99998140140001     \n",
      " Lat:    40.102174002200002        40.727359237400002     \n",
      " Lines:         2952        9704\n",
      " Pixels:            1       10812\n",
      " Max DEM height:    4331.12598    \n",
      " Primary iterations:           25\n",
      " Secondary iterations:           10\n",
      " Distance threshold :    5.0000000000000003E-002\n",
      " Processing line:            1   7593.3146201120417     \n",
      " Dopplers:    0.0000000000000000        0.0000000000000000        0.0000000000000000     \n",
      " Processing line:         1001   7593.2789330875676     \n",
      " Dopplers:    0.0000000000000000        0.0000000000000000        0.0000000000000000     \n",
      " Total convergence:    36670637  out of     38968696\n",
      "API close:  geom_reference/IW3/lat_01.rdr\n",
      "API open (R): geom_reference/IW3/lat_01.rdr\n",
      "API close:  geom_reference/IW3/lat_01.rdr\n",
      "API close:  geom_reference/IW3/lon_01.rdr\n",
      "API open (R): geom_reference/IW3/lon_01.rdr\n",
      "API close:  geom_reference/IW3/lon_01.rdr\n",
      "API close:  geom_reference/IW3/hgt_01.rdr\n",
      "API open (R): geom_reference/IW3/hgt_01.rdr\n",
      "API close:  geom_reference/IW3/hgt_01.rdr\n",
      "API close:  geom_reference/IW3/los_01.rdr\n",
      "API open (R): geom_reference/IW3/los_01.rdr\n",
      "API close:  geom_reference/IW3/los_01.rdr\n",
      "GDAL close: usgs_10m.dem.wgs84.vrt\n",
      "2022-09-06 16:24:34,673 - isce.topsinsar.topo - INFO - \n",
      "####################################################################################################\n",
      "    runTopo\n",
      "----------------------------------------------------------------------------------------------------\n",
      "topo.Bounding box for burst 0 - IW-3 = [40.25818723979505, 40.56696448239103, -106.02050989296794, -104.97437719948798]\n",
      "topo.Dem Used = usgs_10m.dem.wgs84\n",
      "topo.Number of common bursts IW-3 = 1\n",
      "topo.Number of lines for burst 0 - IW-3 = 1517\n",
      "topo.Number of pixels for bursts 0 - IW-3 = 25688\n",
      "topo.Overall bounding box = [40.25818723979505, 40.56696448239103, -106.02050989296794, -104.97437719948798]\n",
      "####################################################################################################\n",
      "Dumping the application's pickle object _insar to file  PICKLE/topo\n",
      "The remaining steps are (in order):  ['subsetoverlaps', 'coarseoffsets', 'coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "CPU times: user 1.04 s, sys: 180 ms, total: 1.22 s\n",
      "Wall time: 1min 52s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "!topsApp.py --dostep=topo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "97c17bdf-8916-483e-ab44-210ebbfc84c7",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "2022-09-06 16:24:35,297 - isce.insar - INFO - ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "Step processing\n",
      "Running step subsetoverlaps\n",
      "Dumping the application's pickle object _insar to file  PICKLE/subsetoverlaps\n",
      "The remaining steps are (in order):  ['coarseoffsets', 'coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step coarseoffsets\n",
      "Dumping the application's pickle object _insar to file  PICKLE/coarseoffsets\n",
      "The remaining steps are (in order):  ['coarseresamp', 'overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step coarseresamp\n",
      "Dumping the application's pickle object _insar to file  PICKLE/coarseresamp\n",
      "The remaining steps are (in order):  ['overlapifg', 'prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step overlapifg\n",
      "Dumping the application's pickle object _insar to file  PICKLE/overlapifg\n",
      "The remaining steps are (in order):  ['prepesd', 'esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step prepesd\n",
      "Dumping the application's pickle object _insar to file  PICKLE/prepesd\n",
      "The remaining steps are (in order):  ['esd', 'rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step esd\n",
      "Dumping the application's pickle object _insar to file  PICKLE/esd\n",
      "The remaining steps are (in order):  ['rangecoreg', 'fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step rangecoreg\n",
      "Dumping the application's pickle object _insar to file  PICKLE/rangecoreg\n",
      "The remaining steps are (in order):  ['fineoffsets', 'fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step fineoffsets\n",
      "2022-09-06 16:24:35,417 - isce.topsinsar.fineoffsets - INFO - IW3 - Burst 0 of reference matched with Burst 0 of secondary\n",
      "GDAL open (R): geom_reference/IW3/lat_01.rdr.vrt\n",
      "GDAL open (R): geom_reference/IW3/lon_01.rdr.vrt\n",
      "GDAL open (R): geom_reference/IW3/hgt_01.rdr.vrt\n",
      "2022-09-06 16:24:35,436 - isce.topsinsar.fineoffsets - INFO - Additional time offset applied in geo2rdr: 0.0 secs\n",
      "2022-09-06 16:24:35,436 - isce.topsinsar.fineoffsets - INFO - Additional range offset applied in geo2rdr: 0.0 m\n",
      "Turning off bistatic delay correction term by default.\n",
      "API open (WR): fine_offsets/IW3/range_01.off\n",
      "API open (WR): fine_offsets/IW3/azimuth_01.off\n",
      " Orbit interpolation method: hermite\n",
      " threads           8\n",
      " Starting Acquisition time:    3737.0287560000002     \n",
      " Stop Acquisition time:    3740.1449793508000     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901705.73182661750     \n",
      " Far  Range in m:    961545.19386730995     \n",
      " Range sample spacing in m:    2.3295621147153232     \n",
      " Radar Image Lines:         1517\n",
      " Radar Image Width:        25688\n",
      " reading dem ...\n",
      " Geocoded Lines:          1517\n",
      " Geocoded Samples:       25688\n",
      " Dopplers:    0.0000000000000000        0.0000000000000000     \n",
      " geo2rdr on            8  threads...\n",
      " Processing line:            1           0\n",
      " Processing line:         1001       85579\n",
      " Number of pixels outside the image:       104708\n",
      " Number of pixels with valid data:       33801373\n",
      " Number of pixels that converged:           25498\n",
      " elapsed time =    29.1484375      seconds\n",
      "API close:  fine_offsets/IW3/range_01.off\n",
      "API open (R): fine_offsets/IW3/range_01.off\n",
      "API close:  fine_offsets/IW3/range_01.off\n",
      "API close:  fine_offsets/IW3/azimuth_01.off\n",
      "API open (R): fine_offsets/IW3/azimuth_01.off\n",
      "API close:  fine_offsets/IW3/azimuth_01.off\n",
      "GDAL close: geom_reference/IW3/lat_01.rdr.vrt\n",
      "GDAL close: geom_reference/IW3/lon_01.rdr.vrt\n",
      "GDAL close: geom_reference/IW3/hgt_01.rdr.vrt\n",
      "Dumping the application's pickle object _insar to file  PICKLE/fineoffsets\n",
      "The remaining steps are (in order):  ['fineresamp', 'ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step fineresamp\n",
      "Shifts IW-3:  {0: 0}\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Chi squared: 0.000032\n",
      "Polynomial Order: 5 - by - 3 \n",
      "11987.4\t-610.308\t18.7998\t0.8812\t\n",
      "-47443.6\t2443.93\t-92.2028\t-3.78314\t\n",
      "46942.9\t-2446.29\t108.848\t4.02728\t\n",
      "-2.05497e-09\t2.30956e-09\t-6.20131e-10\t0\t\n",
      "1.45884e-09\t-8.31376e-10\t0\t0\t\n",
      "-3.81988e-10\t0\t0\t0\t\n",
      "Misfit radians - Max: 0.00011659791380225215 , Min : -0.00022593304129259195 \n",
      "2022-09-06 16:25:04,765 - isce.stdproc.resamp_slc - WARNING - The variable INPUT_LINES has been set to the default value 1517 which is the number of lines in the slc image.\n",
      "2022-09-06 16:25:04,765 - isce.stdproc.resamp_slc - WARNING - The variable INPUT_WIDTH has been set to the default value 25688 which is the width of the slc image.\n",
      "2022-09-06 16:25:04,766 - isce.stdproc.resamp_slc - WARNING - No flattening requested\n",
      "GDAL open (R): secondary/IW3/burst_01.slc.vrt\n",
      "API open (WR): fine_coreg/IW3/burst_01.slc\n",
      "No Range Carrier provided.\n",
      "Assuming zero range carrier.\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 5 - by - 3 \n",
      "11987.4\t-610.308\t18.7998\t0.8812\t\n",
      "-47443.6\t2443.93\t-92.2028\t-3.78314\t\n",
      "46942.9\t-2446.29\t108.848\t4.02728\t\n",
      "-2.05497e-09\t2.30956e-09\t-6.20131e-10\t0\t\n",
      "1.45884e-09\t-8.31376e-10\t0\t0\t\n",
      "-3.81988e-10\t0\t0\t0\t\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      "GDAL open (R): fine_offsets/IW3/range_01.off.vrt\n",
      "GDAL open (R): fine_offsets/IW3/azimuth_01.off.vrt\n",
      "Polynomial Order: 0 - by - 2 \n",
      "-0.152073\t210.32\t-102793\t\n",
      "  \n",
      "  << Resample one image to another image coordinates >>\n",
      "  \n",
      " Input Image Dimensions: \n",
      "       25688  pixels\n",
      "        1517 lines\n",
      "  \n",
      " Output Image Dimensions: \n",
      "       25688 pixels\n",
      "        1517 lines\n",
      "   \n",
      " Number of threads:            8\n",
      " Complex data interpolation\n",
      " Initializing Sinc interpolator\n",
      " Azimuth Carrier Poly\n",
      "Polynomial Order: 5 - by - 3 \n",
      "11987.4\t-610.308\t18.7998\t0.8812\t\n",
      "-47443.6\t2443.93\t-92.2028\t-3.78314\t\n",
      "46942.9\t-2446.29\t108.848\t4.02728\t\n",
      "-2.05497e-09\t2.30956e-09\t-6.20131e-10\t0\t\n",
      "1.45884e-09\t-8.31376e-10\t0\t0\t\n",
      "-3.81988e-10\t0\t0\t0\t\n",
      " Range Carrier Poly\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      " Range offsets poly\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      " Azimuth offsets poly\n",
      "Polynomial Order: 0 - by - 0 \n",
      "0\t\n",
      " Doppler poly\n",
      "Polynomial Order: 0 - by - 2 \n",
      "-0.152073\t210.32\t-102793\t\n",
      " Reading in the image\n",
      " At line         1000\n",
      " Interpolating image\n",
      " At line         1000\n",
      " Elapsed time:    22.8164062    \n",
      "GDAL close: fine_offsets/IW3/range_01.off.vrt\n",
      "GDAL close: fine_offsets/IW3/azimuth_01.off.vrt\n",
      "GDAL close: secondary/IW3/burst_01.slc.vrt\n",
      "API close:  fine_coreg/IW3/burst_01.slc\n",
      "API open (R): fine_coreg/IW3/burst_01.slc\n",
      "API close:  fine_coreg/IW3/burst_01.slc\n",
      "Adjust valid samples\n",
      "Before:  538 23652\n",
      "Offsets :  33.738983154296875 36.498172760009766\n",
      "Adjust valid lines\n",
      "Before:  28 1463\n",
      "Offsets :  -1.298854947090149 -1.177946925163269\n",
      "After:  34 1455\n",
      "Dumping the application's pickle object _insar to file  PICKLE/fineresamp\n",
      "The remaining steps are (in order):  ['ion', 'burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step ion\n",
      "Dumping the application's pickle object _insar to file  PICKLE/ion\n",
      "The remaining steps are (in order):  ['burstifg', 'mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step burstifg\n",
      "GDAL open (R): fine_interferogram/IW3/burst_01.int.vrt\n",
      "API open (WR): fine_interferogram/IW3/burst_01.1alks_6rlks.int\n",
      "GDAL close: fine_interferogram/IW3/burst_01.int.vrt\n",
      "API close:  fine_interferogram/IW3/burst_01.1alks_6rlks.int\n",
      "API open (R): fine_interferogram/IW3/burst_01.1alks_6rlks.int\n",
      "API close:  fine_interferogram/IW3/burst_01.1alks_6rlks.int\n",
      "Writing geotrans to VRT for fine_interferogram/IW3/burst_01.1alks_6rlks.int\n",
      "GDAL open (R): reference/IW3/burst_01.slc.vrt\n",
      "GDAL open (R): fine_coreg/IW3/burst_01.slc.vrt\n",
      "API open (WR): fine_interferogram/IW3/burst_01.cor\n",
      "2022-09-06 16:25:42,447 - isce.mroipac.correlation - INFO - Calculating Correlation\n",
      "Operating on coregistered SLCs. \n",
      "Number of lines : 1517\n",
      "Number of pixels: 25688\n",
      "Processing with box size of 5\n",
      "# correlation weights (range,azimuth): 5 5\n",
      "\n",
      "range correlation weights:\n",
      "index,coefficient: -2  0.333333\n",
      "index,coefficient: -1  0.666667\n",
      "index,coefficient: 0  1\n",
      "index,coefficient: 1  0.666667\n",
      "index,coefficient: 2  0.333333\n",
      "\n",
      "azimuth correlation weights:\n",
      "index,coefficient:  -2  0.333333\n",
      "index,coefficient:  -1  0.666667\n",
      "index,coefficient:  0  1\n",
      "index,coefficient:  1  0.666667\n",
      "index,coefficient:  2  0.333333\n",
      "processing line: 1510essing line: 5000line: 1450\n",
      "output lines:1517\n",
      "API close:  fine_interferogram/IW3/burst_01.cor\n",
      "GDAL close: reference/IW3/burst_01.slc.vrt\n",
      "GDAL close: fine_coreg/IW3/burst_01.slc.vrt\n",
      "Dumping the application's pickle object _insar to file  PICKLE/burstifg\n",
      "The remaining steps are (in order):  ['mergebursts', 'filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step mergebursts\n",
      "Multilooking merged/topophase.flat.full ...\n",
      "GDAL open (R): merged/topophase.flat.full.vrt\n",
      "API open (WR): merged/topophase.flat\n",
      "GDAL close: merged/topophase.flat.full.vrt\n",
      "API close:  merged/topophase.flat\n",
      "API open (R): merged/topophase.flat\n",
      "API close:  merged/topophase.flat\n",
      "Writing geotrans to VRT for merged/topophase.flat\n",
      "Multilooking merged/los.rdr.full ...\n",
      "GDAL open (R): merged/los.rdr.full.vrt\n",
      "API open (WR): merged/los.rdr\n",
      "GDAL close: merged/los.rdr.full.vrt\n",
      "API close:  merged/los.rdr\n",
      "API open (R): merged/los.rdr\n",
      "API close:  merged/los.rdr\n",
      "Writing geotrans to VRT for merged/los.rdr\n",
      "Multilooking merged/topophase.cor.full ...\n",
      "GDAL open (R): merged/topophase.cor.full.vrt\n",
      "API open (WR): merged/topophase.cor\n",
      "GDAL close: merged/topophase.cor.full.vrt\n",
      "API close:  merged/topophase.cor\n",
      "API open (R): merged/topophase.cor\n",
      "API close:  merged/topophase.cor\n",
      "Writing geotrans to VRT for merged/topophase.cor\n",
      "Dumping the application's pickle object _insar to file  PICKLE/mergebursts\n",
      "The remaining steps are (in order):  ['filter', 'unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "CPU times: user 1.12 s, sys: 245 ms, total: 1.37 s\n",
      "Wall time: 1min 32s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "!topsApp.py --start=subsetoverlaps --end=mergebursts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "94f43576-17f1-480d-99d9-209e4a5b1aa3",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "2022-09-06 16:26:07,865 - isce.insar - INFO - ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "Step processing\n",
      "Running step filter\n",
      "2022-09-06 16:26:07,911 - isce.topsinsar.runFilter - INFO - Applying power-spectral filter\n",
      "GDAL open (R): merged/topophase.flat.vrt\n",
      "API open (WR): merged/filt_topophase.flat\n",
      "2022-09-06 16:26:07,928 - isce.mroipac.filter - DEBUG - width: 4281\n",
      "2022-09-06 16:26:07,929 - isce.mroipac.filter - DEBUG - length: 1517\n",
      "2022-09-06 16:26:07,929 - isce.mroipac.filter - DEBUG - input: merged/topophase.flat\n",
      "2022-09-06 16:26:07,929 - isce.mroipac.filter - DEBUG - output: merged/filt_topophase.flat\n",
      "2022-09-06 16:26:07,929 - isce.mroipac.filter - DEBUG - filter strength: 0.5\n",
      "2022-09-06 16:26:07,929 - isce.mroipac.filter - INFO - Filtering interferogram\n",
      "array width, height, offset:  4281  1517     0\n",
      "line:  1504\n",
      "number of lines written to file: 1520\n",
      "Rescaling magnitude\n",
      "line:  1516GDAL close: merged/topophase.flat.vrt\n",
      "API close:  merged/filt_topophase.flat\n",
      "GDAL open (R): merged/filt_topophase.flat.vrt\n",
      "API open (WR): merged/phsig.cor\n",
      "\n",
      " << PS filtering >>\n",
      "\n",
      "\n",
      " interferogram width:  4281  number of lines/patch:  3700\n",
      " start line:        1  number of lines:    1517\n",
      " start sample:      1  end sample:         4281\n",
      " wisdomFile, length =            0\n",
      "\n",
      " azimuth buffer size:                             3700\n",
      " overlap between azimuth patches:                  200\n",
      " total overlap between azimuth patches:            264\n",
      " offset in overlap region for phase  bootstrap:    132\n",
      " lines to increment for the next patch:           3436\n",
      " number of patches:                                  1\n",
      "\n",
      " PATCH:   1   starting line:     0    lines read: 1517\n",
      " starting output line:    1   ending output line: 1517\n",
      "\n",
      "*** Normal Completion  ***\n",
      "\n",
      "GDAL close: merged/filt_topophase.flat.vrt\n",
      "API close:  merged/phsig.cor\n",
      "API open (R): merged/phsig.cor\n",
      "API close:  merged/phsig.cor\n",
      "Dumping the application's pickle object _insar to file  PICKLE/filter\n",
      "The remaining steps are (in order):  ['unwrap', 'unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step unwrap\n",
      "\n",
      "snaphu v1.4.2\n",
      "Reading wrapped phase from file merged/filt_topophase.flat\n",
      "No weight file specified.  Assuming uniform weights\n",
      "Reading correlation data from file merged/phsig.cor\n",
      "Calculating smooth-solution cost parameters\n",
      "Initializing flows with MCF algorithm\n",
      "Integrating phase\n",
      "Writing output to file merged/filt_topophase.unw\n",
      "Growing connected components on second pass\n",
      "\n",
      "snaphu v1.4.2\n",
      "Reading unwrapped phase from file merged/filt_topophase.unw\n",
      "No weight file specified.  Assuming uniform weights\n",
      "Reading correlation data from file merged/phsig.cor\n",
      "Calculating smooth-solution cost parameters\n",
      "Growing connected component mask\n",
      "Writing connected components to file merged/filt_topophase.unw.conncomp\n",
      "API open (R): merged/filt_topophase.unw\n",
      "API close:  merged/filt_topophase.unw\n",
      "GDAL open (R): merged/filt_topophase.unw.vrt\n",
      "GDAL close: merged/filt_topophase.unw.vrt\n",
      "API open (R): merged/filt_topophase.unw.conncomp\n",
      "API close:  merged/filt_topophase.unw.conncomp\n",
      "GDAL open (R): merged/filt_topophase.unw.conncomp.vrt\n",
      "GDAL close: merged/filt_topophase.unw.conncomp.vrt\n",
      "imageMath.py -e='a_0*(abs(b)!=0);a_1*(abs(b)!=0)' --a=tmp.unw --b=merged/filt_topophase.flat -s BIL -o=merged/filt_topophase.unw\n",
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "args:  Namespace(debug=False, dtype='float', equation='a_0*(abs(b)!=0);a_1*(abs(b)!=0)', hh=None, noxml=False, out='merged/filt_topophase.unw', scheme='BIL')\n",
      "files:  ['--a=tmp.unw', '--b=merged/filt_topophase.flat']\n",
      "GDAL open (R): merged/filt_topophase.unw.vrt\n",
      "GDAL close: merged/filt_topophase.unw.vrt\n",
      "Dumping the application's pickle object _insar to file  PICKLE/unwrap\n",
      "The remaining steps are (in order):  ['unwrap2stage', 'geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "Running step unwrap2stage\n",
      "Dumping the application's pickle object _insar to file  PICKLE/unwrap2stage\n",
      "The remaining steps are (in order):  ['geocode', 'denseoffsets', 'filteroffsets', 'geocodeoffsets']\n",
      "CPU times: user 4.4 s, sys: 1.47 s, total: 5.87 s\n",
      "Wall time: 4min 37s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "!topsApp.py --start=filter --end=unwrap2stage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "f4b909e6-5941-4eaa-b184-adf706ea3293",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "2022-09-06 16:30:45,354 - isce.insar - INFO - ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "ISCE VERSION = 2.6.1, RELEASE_SVN_REVISION = ,RELEASE_DATE = 20220811, CURRENT_SVN_REVISION = \n",
      "Step processing\n",
      "Running step geocode\n",
      "2022-09-06 16:30:45,404 - isce.topsinsar.runGeocode - INFO - Geocoding Image\n",
      "Number of products to geocode:  3\n",
      "Output:  merged/topophase.cor.geo\n",
      "API open (WR): merged/dem.crop\n",
      "API open (WR): merged/topophase.cor.geo\n",
      "GDAL open (R): merged/topophase.cor.vrt\n",
      "GDAL open (R): usgs_10m.dem.wgs84.vrt\n",
      " Using nearest neighbor interpolation\n",
      " threads           8\n",
      " Starting Acquisition time:    3736.5043129999999     \n",
      " Stop Acquisition time:    3739.6205363507997     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901711.55573190434     \n",
      " Far  Range in m:    961534.71083779389     \n",
      " Range sample spacing in m:    13.977372688291940     \n",
      " Input Lines:         1517\n",
      " Input Width:         4281\n",
      " reading interferogram ...\n",
      " Geocoded Lines:          3512\n",
      " Geocoded Samples:       12431\n",
      " Initializing Nearest Neighbor Interpolator\n",
      " geocoding on            8  threads...\n",
      " Number of pixels with outside DEM:             0\n",
      " Number of pixels outside the image:     20919008\n",
      " Number of pixels with valid data:       20550650\n",
      " elapsed time =    25.4492188      seconds\n",
      " Using nearest neighbor interpolation\n",
      " threads           8\n",
      " Starting Acquisition time:    3736.5043129999999     \n",
      " Stop Acquisition time:    3739.6205363507997     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901711.55573190434     \n",
      " Far  Range in m:    961534.71083779389     \n",
      " Range sample spacing in m:    13.977372688291940     \n",
      " Input Lines:         1517\n",
      " Input Width:         4281\n",
      " reading interferogram ...\n",
      " Geocoded Lines:          3512\n",
      " Geocoded Samples:       12431\n",
      " Initializing Nearest Neighbor Interpolator\n",
      " geocoding on            8  threads...\n",
      " Number of pixels with outside DEM:             0\n",
      " Number of pixels outside the image:     20971610\n",
      " Number of pixels with valid data:       20586659\n",
      " elapsed time =    25.3007812      seconds\n",
      "GDAL close: usgs_10m.dem.wgs84.vrt\n",
      "GDAL close: merged/topophase.cor.vrt\n",
      "API close:  merged/dem.crop\n",
      "API close:  merged/topophase.cor.geo\n",
      "API open (R): merged/topophase.cor.geo\n",
      "API close:  merged/topophase.cor.geo\n",
      "Writing geotrans to VRT for merged/topophase.cor.geo\n",
      "Output:  merged/filt_topophase.unw.geo\n",
      "API open (WR): merged/dem.crop\n",
      "API open (WR): merged/filt_topophase.unw.geo\n",
      "GDAL open (R): merged/filt_topophase.unw.vrt\n",
      "GDAL open (R): usgs_10m.dem.wgs84.vrt\n",
      " Using nearest neighbor interpolation\n",
      " threads           8\n",
      " Starting Acquisition time:    3736.5043129999999     \n",
      " Stop Acquisition time:    3739.6205363507997     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901711.55573190434     \n",
      " Far  Range in m:    961534.71083779389     \n",
      " Range sample spacing in m:    13.977372688291940     \n",
      " Input Lines:         1517\n",
      " Input Width:         4281\n",
      " reading interferogram ...\n",
      " Geocoded Lines:          3512\n",
      " Geocoded Samples:       12431\n",
      " Initializing Nearest Neighbor Interpolator\n",
      " geocoding on            8  threads...\n",
      " Number of pixels with outside DEM:             0\n",
      " Number of pixels outside the image:     20785400\n",
      " Number of pixels with valid data:       20291401\n",
      " elapsed time =    25.4179688      seconds\n",
      " Using nearest neighbor interpolation\n",
      " threads           8\n",
      " Starting Acquisition time:    3736.5043129999999     \n",
      " Stop Acquisition time:    3739.6205363507997     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901711.55573190434     \n",
      " Far  Range in m:    961534.71083779389     \n",
      " Range sample spacing in m:    13.977372688291940     \n",
      " Input Lines:         1517\n",
      " Input Width:         4281\n",
      " reading interferogram ...\n",
      " Geocoded Lines:          3512\n",
      " Geocoded Samples:       12431\n",
      " Initializing Nearest Neighbor Interpolator\n",
      " geocoding on            8  threads...\n",
      " Number of pixels with outside DEM:             0\n",
      " Number of pixels outside the image:     20879778\n",
      " Number of pixels with valid data:       20593847\n",
      " elapsed time =    25.5039062      seconds\n",
      "GDAL close: merged/filt_topophase.unw.vrt\n",
      "API close:  merged/dem.crop\n",
      "API close:  merged/filt_topophase.unw.geo\n",
      "API open (R): merged/filt_topophase.unw.geo\n",
      "API close:  merged/filt_topophase.unw.geo\n",
      "Writing geotrans to VRT for merged/filt_topophase.unw.geo\n",
      "Output:  merged/filt_topophase.flat.geo\n",
      "API open (WR): merged/dem.crop\n",
      "API open (WR): merged/filt_topophase.flat.geo\n",
      "GDAL open (R): merged/filt_topophase.flat.vrt\n",
      " Using Sinc interpolation\n",
      " threads           8\n",
      " Starting Acquisition time:    3736.5043129999999     \n",
      " Stop Acquisition time:    3739.6205363507997     \n",
      " Azimuth line spacing in secs:    2.0555562999999980E-003\n",
      " Near Range in m:    901711.55573190434     \n",
      " Far  Range in m:    961534.71083779389     \n",
      " Range sample spacing in m:    13.977372688291940     \n",
      " Input Lines:         1517\n",
      " Input Width:         4281\n",
      " reading interferogram ...\n",
      " Geocoded Lines:          3512\n",
      " Geocoded Samples:       12431\n",
      " Initializing Sinc Interpolator\n",
      " geocoding on            8  threads...\n",
      " Number of pixels with outside DEM:             0\n",
      " Number of pixels outside the image:     20829463\n",
      " Number of pixels with valid data:       19858828\n",
      " elapsed time =    27.3085938      seconds\n",
      "GDAL close: merged/filt_topophase.flat.vrt\n",
      "API close:  merged/dem.crop\n",
      "API close:  merged/filt_topophase.flat.geo\n",
      "API open (R): merged/filt_topophase.flat.geo\n",
      "API close:  merged/filt_topophase.flat.geo\n",
      "Writing geotrans to VRT for merged/filt_topophase.flat.geo\n",
      "2022-09-06 16:32:54,728 - isce.topsinsar.runGeocode - INFO - \n",
      "####################################################################################################\n",
      "    runGeocode\n",
      "----------------------------------------------------------------------------------------------------\n",
      "geocode.Azimuth looks = 1\n",
      "geocode.Dem Used = usgs_10m.dem.wgs84\n",
      "geocode.East = -104.86942583540001\n",
      "geocode.Geocoding:  = merged/filt_topophase.flat\n",
      "geocode.Length = 1517\n",
      "geocode.North = 40.577451818\n",
      "geocode.Output file:  = merged/filt_topophase.flat.geo\n",
      "geocode.Range looks = 6\n",
      "geocode.South = 40.2522666068\n",
      "geocode.West = -106.020444446\n",
      "geocode.Width = 4281\n",
      "####################################################################################################\n",
      "Dumping the application's pickle object _insar to file  PICKLE/geocode\n",
      "The remaining steps are (in order):  ['denseoffsets', 'filteroffsets', 'geocodeoffsets']\n"
     ]
    }
   ],
   "source": [
    "!topsApp.py --dostep=geocode"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "652af0c4-afa2-4042-a0a0-8c2cdcb5e953",
   "metadata": {},
   "source": [
    "## extract wrapped phase from complex values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "c4b05bbb-72ee-43f9-a3ef-ff31d7dfe8bf",
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir('/home/jovyan/rmnp_landslide/proc/merged/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "50d5f484-3fb4-4cb3-8f44-337622b8d2e3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is the Open Source version of ISCE.\n",
      "Some of the workflows depend on a separate licensed package.\n",
      "To obtain the licensed package, please make a request for ISCE\n",
      "through the website: https://download.jpl.nasa.gov/ops/request/index.cfm.\n",
      "Alternatively, if you are a member, or can become a member of WinSAR\n",
      "you may be able to obtain access to a version of the licensed sofware at\n",
      "https://winsar.unavco.org/software/isce\n",
      "Writing geotrans to VRT for merged/filt_topophase.flat.geo\n",
      "Traceback (most recent call last):\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/xml/etree/ElementTree.py\", line 786, in _get_writer\n",
      "    write = file_or_filename.write\n",
      "AttributeError: 'str' object has no attribute 'write'\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications/isce2gis.py\", line 88, in <module>\n",
      "    isce2vrt(inps.infile)\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/applications/isce2gis.py\", line 51, in isce2vrt\n",
      "    img.renderVRT()\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/site-packages/isce/components/isceobj/Image/Image.py\", line 578, in renderVRT\n",
      "    tree.write(outfile, encoding='unicode')\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/xml/etree/ElementTree.py\", line 756, in write\n",
      "    with _get_writer(file_or_filename, enc_lower) as write:\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/contextlib.py\", line 113, in __enter__\n",
      "    return next(self.gen)\n",
      "  File \"/home/jovyan/.local/envs/insar_analysis/lib/python3.8/xml/etree/ElementTree.py\", line 790, in _get_writer\n",
      "    file = open(file_or_filename, \"w\")\n",
      "FileNotFoundError: [Errno 2] No such file or directory: 'merged/filt_topophase.flat.geo.vrt'\n",
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     ]
    }
   ],
   "source": [
    "!isce2gis.py vrt -i filt_topophase.flat.geo\n",
    "\n",
    "!gdal_calc.py --type Float32 -A filt_topophase.flat.geo.vrt --calc=\"numpy.angle(A)\" --outfile=filt_topophase.flat.geo.phs.tif --NoDataValue=0.0 --overwrite"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "insar_analysis [conda env:.local-insar_analysis]",
   "language": "python",
   "name": "conda-env-.local-insar_analysis-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}