Ensure consistency for comment style and indentation (#75)

Co-authored-by: rzinke <robert.zinke@jpl.nasa.gov>

Author: rzinke

methods/coseismic/Coseismic_Requirement_Validation.ipynb

@@ -600,11 +600,11 @@
     "command = 'timeseries2velocity.py ' + timeseries_filename + function_str\n",
     "process = subprocess.run(command, shell=True)\n",
     "\n",
-    "# load velocity file\n",
+    "# Load velocity file\n",
     "insar_velocities,_ = readfile.read(vel_file, datasetName = 'velocity')  # read velocity file\n",
     "insar_velocities = insar_velocities * 1000.  # convert InSAR velocities from m/yr to mm/yr\n",
     "\n",
-    "# set masked pixels to NaN\n",
+    "# Set masked pixels to NaN\n",
     "msk,_ = readfile.read(msk_file)\n",
     "insar_velocities[msk == 0] = np.nan\n",
     "insar_velocities[insar_velocities == 0] = np.nan"
@@ -739,13 +739,15 @@
     "bbox = sitedata['sites'][site]['analysis_region'].replace(\"'\",\"\").split()\n",
     "lat0 = (float(bbox[0]) + float(bbox[1]))/2\n",
     "lon0 = (float(bbox[2]) + float(bbox[3]))/2\n",
+    "\n",
     "# Identify geometry file x/y location associated with center lat/lon\n",
     "geom_obj = mintpy_dir + '/inputs/geometryGeo.h5'\n",
     "atr = readfile.read_attribute(geom_obj)\n",
     "coord = ut.coordinate(atr, lookup_file=geom_obj)\n",
     "y, x = coord.geo2radar(lat0, lon0)[0:2]\n",
     "y = max(0, y);  y = min(int(atr['LENGTH'])-1, y)\n",
     "x = max(0, x);  x = min(int(atr['WIDTH'])-1, x)\n",
+    "\n",
     "# Write out inclination/azimuth at specified x/y location\n",
     "kwargs = dict(box=(x,y,x+1,y+1))\n",
     "inc_angle = readfile.read(geom_obj, datasetName='incidenceAngle', **kwargs)[0][0,0]\n",
@@ -1329,7 +1331,7 @@
    },
    "outputs": [],
    "source": [
-    "# use the non-earthquake displacement as the insar_displacment for statistics and convert to mm\n",
+    "# Use the non-earthquake displacement as the insar_displacment for statistics and convert to mm\n",
     "noEQdataset = 'step' + sitedata['sites'][site]['noEarthquakeDate']\n",
     "noEQstep, insar_metadata = readfile.read(vel_file, datasetName = noEQdataset)  #read coseismic step \n",
     "(S,N,W,E) = ut.four_corners(insar_metadata)\n",
@@ -1340,12 +1342,12 @@
     "ifgs_date = np.array([noEQdate])  # only one non-earthquake date for now\n",
     "n_ifgs = insar_displacement.shape[0]\n",
     "\n",
-    "# mask out no-data areas\n",
+    "# Mask out no-data areas\n",
     "msk, _ = readfile.read(msk_file)\n",
     "insar_displacement[msk == 0] = np.nan\n",
     "insar_displacement[insar_displacement == 0] = np.nan\n",
     "\n",
-    "# display map of data after masking\n",
+    "# Display map of data after masking\n",
     "cmap = plt.get_cmap('RdBu')\n",
     "fig, ax = plt.subplots(figsize=[18, 5.5])\n",
     "img1 = ax.imshow(insar_displacement, cmap=cmap, interpolation='nearest', extent=(W, E, S, N))\n",
@@ -1638,12 +1640,12 @@
    },
    "outputs": [],
    "source": [
-    "# grab the time-series file used for time function estimation given the template setup\n",
+    "# Grab the time-series file used for time function estimation given the template setup\n",
     "template = readfile.read_template(os.path.join(mintpy_dir, 'smallbaselineApp.cfg'))\n",
     "template = ut.check_template_auto_value(template)\n",
     "insar_ts_file = TimeSeriesAnalysis.get_timeseries_filename(template, mintpy_dir)['velocity']['input']\n",
     "\n",
-    "# read the time-series file\n",
+    "# Read the time-series file\n",
     "insar_ts, atr = readfile.read(insar_ts_file, datasetName='timeseries')\n",
     "mask = readfile.read(os.path.join(mintpy_dir, 'maskTempCoh.h5'))[0]\n",
     "print(f'reading timeseries from file: {insar_ts_file}')\n",
@@ -1654,7 +1656,7 @@
     "date0, date1 = date_list[0], date_list[-1]\n",
     "insar_dates = ptime.date_list2vector(date_list)[0]\n",
     "\n",
-    "# spatial reference\n",
+    "# Spatial reference\n",
     "coord = ut.coordinate(atr)\n",
     "ref_site = sitedata['sites'][site]['gps_ref_site_name']\n",
     "ref_gnss_obj = gnss_stns[ref_site]\n",
@@ -1670,8 +1672,8 @@
     "for i, site_name in enumerate(site_names):\n",
     "    prog_bar.update(i+1, suffix=f'{site_name} {i+1}/{num_site}')\n",
     "\n",
-    "    ## read data\n",
-    "    # recall gnss station displacements with outliers removed\n",
+    "    ## Read data\n",
+    "    # Recall gnss station displacements with outliers removed\n",
     "    gnss_obj = gnss_stns[site_name]\n",
     "    gnss_lalo = (gnss_obj.site_lat, gnss_obj.site_lon)\n",
     "\n",
@@ -1683,10 +1685,10 @@
     "        idx2 = np.where(ref_gnss_obj.dates == date_i)[0][0]\n",
     "        gnss_dis[i] = gnss_obj.dis_los[idx1] - ref_gnss_obj.dis_los[idx2]\n",
     "    \n",
-    "    # shift GNSS to zero-mean in time [for plotting purpose]\n",
+    "    # Shift GNSS to zero-mean in time [for plotting purpose]\n",
     "    gnss_dis -= np.nanmedian(gnss_dis)\n",
     "\n",
-    "    # read InSAR\n",
+    "    # Read InSAR\n",
     "    y, x = coord.geo2radar(gnss_lalo[0], gnss_lalo[1])[:2]\n",
     "    insar_dis = insar_ts[:, y, x] - ref_insar_dis\n",
     "    # apply a constant shift in time to fit InSAR to GNSS\n",
@@ -1696,7 +1698,7 @@
     "        gnss_flag = [x in comm_dates for x in gnss_dates]\n",
     "        insar_dis -= np.nanmedian(insar_dis[insar_flag] - gnss_dis[gnss_flag])\n",
     "\n",
-    "    ## plot figure\n",
+    "    ## Plot figure\n",
     "    if gnss_dis.size > 0 and np.any(~np.isnan(insar_dis)):\n",
     "        fig, ax = plt.subplots(figsize=(10, 3))\n",
     "        ax.axhline(color='grey',linestyle='dashed', linewidth=2)\n",
@@ -1706,6 +1708,7 @@
     "        ax.set_title(f\"Station Name: {site_name}\") \n",
     "        ax.set_ylabel('LOS displacement [mm]')\n",
     "        ax.legend()\n",
+    "\n",
     "prog_bar.close()\n",
     "plt.show()"
    ]

methods/secular/Secular_Requirement_Validation.ipynb

@@ -627,11 +627,11 @@
     "command = 'timeseries2velocity.py ' + timeseries_filename + function_str\n",
     "process = subprocess.run(command, shell=True)\n",
     "\n",
-    "# load velocity file\n",
+    "# Load velocity file\n",
     "insar_velocities,_ = readfile.read(vel_file, datasetName = 'velocity')  # read velocity file\n",
     "insar_velocities = insar_velocities * 1000.  # convert InSAR velocities from m/yr to mm/yr\n",
     "\n",
-    "# set masked pixels to NaN\n",
+    "# Set masked pixels to NaN\n",
     "msk,_ = readfile.read(msk_file)\n",
     "insar_velocities[msk == 0] = np.nan\n",
     "insar_velocities[insar_velocities == 0] = np.nan"
@@ -943,14 +943,14 @@
    },
    "outputs": [],
    "source": [
-    "# reference GNSS stations to GNSS reference site\n",
+    "# Reference GNSS stations to GNSS reference site\n",
     "ref_site = sitedata['sites'][site]['gps_ref_site_name']\n",
     "if sitedata['sites'][site]['gps_ref_site_name'] == 'auto':\n",
     "    ref_site = [*gnss_stns][0]\n",
     "\n",
     "print(\"Using GNSS reference station: \", ref_site)\n",
     "\n",
-    "# re-reference GNSS sites\n",
+    "# Re-reference GNSS sites\n",
     "if 'vel_mm_yr' in gnss_stns[ref_site].vel_dict:\n",
     "    ref_vel = gnss_stns[ref_site].vel_dict['vel_mm_yr']\n",
     "\n",
@@ -963,12 +963,12 @@
     "        # Remove non-referenced station data to avoid future confusion\n",
     "        del gnss_stn.vel_dict['vel_mm_yr']\n",
     "\n",
-    "# reference InSAR to GNSS reference site\n",
+    "# Reference InSAR to GNSS reference site\n",
     "ref_site_lat, ref_site_lon = gnss_stns[ref_site].get_site_lat_lon()\n",
     "ref_y, ref_x = ut.coordinate(insar_metadata).geo2radar(ref_site_lat, ref_site_lon)[:2]\n",
     "insar_velocities = insar_velocities - insar_velocities[ref_y, ref_x]\n",
     "\n",
-    "# plot GNSS stations on InSAR velocity field\n",
+    "# Plot GNSS stations on InSAR velocity field\n",
     "vmin, vmax = -25, 25\n",
     "cmap = plt.get_cmap('RdBu_r')\n",
     "\n",
@@ -1028,27 +1028,27 @@
    },
    "outputs": [],
    "source": [
-    "#Set Parameters\n",
+    "# Set Parameters\n",
     "pixel_radius = 5   #number of InSAR pixels to average for comparison with GNSS\n",
     "\n",
-    "#Loop over GNSS station locations\n",
+    "# Loop over GNSS station locations\n",
     "for site_name in site_names:\n",
     "    gnss_stn = gnss_stns[site_name]\n",
     "    \n",
-    "    # convert GNSS station lat/lon information to InSAR x/y grid\n",
+    "    # Convert GNSS station lat/lon information to InSAR x/y grid\n",
     "    stn_lat, stn_lon = gnss_stn.get_site_lat_lon()\n",
     "    stn_y, stn_x = ut.coordinate(insar_metadata).geo2radar(stn_lat, stn_lon)[:2]\n",
     "    \n",
-    "    # get velocities and residuals\n",
+    "    # Get velocities and residuals\n",
     "    gnss_site_vel = gnss_stn.vel_dict['gnss_site_vel']\n",
-    "    #Caution: If you expand the radius parameter farther than the bounding grid it will break. \n",
-    "    #To fix, remove the station in section 4 when the site_names list is filtered\n",
+    "    # Caution: If you expand the radius parameter farther than the bounding grid it will break. \n",
+    "    # To fix, remove the station in section 4 when the site_names list is filtered\n",
     "    vel_px_rad = insar_velocities[stn_y-pixel_radius:stn_y+1+pixel_radius, \n",
     "                                  stn_x-pixel_radius:stn_x+1+pixel_radius]\n",
     "    insar_site_vel = np.median(vel_px_rad)\n",
     "    residual = gnss_site_vel - insar_site_vel\n",
     "\n",
-    "    # populate data structure\n",
+    "    # Populate data structure\n",
     "    gnss_stn.vel_dict['insar_site_vel'] = insar_site_vel\n",
     "    gnss_stn.vel_dict['residual'] = residual\n",
     "\n",
@@ -1076,7 +1076,7 @@
     "stn_dist_list = []\n",
     "n_gnss_sites = len(site_names)\n",
     "\n",
-    "# loop over stations\n",
+    "# Loop over stations\n",
     "for i in range(n_gnss_sites - 1):\n",
     "    stn1 = gnss_stns[site_names[i]]\n",
     "    for j in range(i + 1, n_gnss_sites):\n",
@@ -1195,17 +1195,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# use the assumed non-earthquake displacement as the insar_displacment for statistics and convert to mm\n",
+    "# Use the assumed non-earthquake displacement as the insar_displacment for statistics and convert to mm\n",
     "insar_velocities,_ = readfile.read(vel_file, datasetName = 'velocity')  #read velocity\n",
     "velStart = sitedata['sites'][site]['download_start_date']\n",
     "insar_velocities = insar_velocities * 1000.  # convert velocities from m to mm\n",
     "\n",
-    "# set masked pixels to NaN\n",
+    "# Set masked pixels to NaN\n",
     "msk,_ = readfile.read(msk_file)\n",
     "insar_velocities[msk == 0] = np.nan\n",
     "insar_velocities[insar_velocities == 0] = np.nan\n",
     "\n",
-    "# display map of velocity data after masking\n",
+    "# Display map of velocity data after masking\n",
     "cmap = plt.get_cmap('RdBu_r')\n",
     "fig, ax = plt.subplots(figsize=[18, 5.5])\n",
     "img1 = ax.imshow(insar_velocities, cmap=cmap, vmin=-20, vmax=20, interpolation='nearest', extent=(W, E, S, N))\n",
@@ -1438,12 +1438,12 @@
    },
    "outputs": [],
    "source": [
-    "# grab the time-series file used for time function estimation given the template setup\n",
+    "# Grab the time-series file used for time function estimation given the template setup\n",
     "template = readfile.read_template(os.path.join(mintpy_dir, 'smallbaselineApp.cfg'))\n",
     "template = ut.check_template_auto_value(template)\n",
     "insar_ts_file = TimeSeriesAnalysis.get_timeseries_filename(template, mintpy_dir)['velocity']['input']\n",
     "\n",
-    "# read the time-series file\n",
+    "# Read the time-series file\n",
     "insar_ts, atr = readfile.read(insar_ts_file, datasetName='timeseries')\n",
     "mask = readfile.read(os.path.join(mintpy_dir, 'maskTempCoh.h5'))[0]\n",
     "print(f'reading timeseries from file: {insar_ts_file}')\n",
@@ -1454,7 +1454,7 @@
     "date0, date1 = date_list[0], date_list[-1]\n",
     "insar_dates = ptime.date_list2vector(date_list)[0]\n",
     "\n",
-    "# spatial reference\n",
+    "# Spatial reference\n",
     "coord = ut.coordinate(atr)\n",
     "ref_site = sitedata['sites'][site]['gps_ref_site_name']\n",
     "ref_gnss_obj = gnss_stns[ref_site]\n",
@@ -1470,33 +1470,33 @@
     "for i, site_name in enumerate(site_names):\n",
     "    prog_bar.update(i+1, suffix=f'{site_name} {i+1}/{num_site}')\n",
     "\n",
-    "    ## read data\n",
-    "    # recall gnss station displacements with outliers removed\n",
+    "    ## Read data\n",
+    "    # Recall gnss station displacements with outliers removed\n",
     "    gnss_obj = gnss_stns[site_name]\n",
     "    gnss_lalo = (gnss_obj.site_lat, gnss_obj.site_lon)\n",
     "\n",
-    "    # get relative LOS displacement on common dates\n",
+    "    # Get relative LOS displacement on common dates\n",
     "    gnss_dates = np.array(sorted(list(set(gnss_obj.dates) & set(ref_gnss_obj.dates))))\n",
     "    gnss_dis = np.zeros(gnss_dates.shape, dtype=np.float32)\n",
     "    for i, date_i in enumerate(gnss_dates):\n",
     "        idx1 = np.where(gnss_obj.dates == date_i)[0][0]\n",
     "        idx2 = np.where(ref_gnss_obj.dates == date_i)[0][0]\n",
     "        gnss_dis[i] = gnss_obj.dis_los[idx1] - ref_gnss_obj.dis_los[idx2]\n",
     "    \n",
-    "    # shift GNSS to zero-mean in time [for plotting purpose]\n",
+    "    # Shift GNSS to zero-mean in time [for plotting purpose]\n",
     "    gnss_dis -= np.nanmedian(gnss_dis)\n",
     "\n",
-    "    # read InSAR\n",
+    "    # Read InSAR\n",
     "    y, x = coord.geo2radar(gnss_lalo[0], gnss_lalo[1])[:2]\n",
     "    insar_dis = insar_ts[:, y, x] - ref_insar_dis\n",
-    "    # apply a constant shift in time to fit InSAR to GNSS\n",
+    "    # Apply a constant shift in time to fit InSAR to GNSS\n",
     "    comm_dates = sorted(list(set(gnss_dates) & set(insar_dates)))\n",
     "    if comm_dates:\n",
     "        insar_flag = [x in comm_dates for x in insar_dates]\n",
     "        gnss_flag = [x in comm_dates for x in gnss_dates]\n",
     "        insar_dis -= np.nanmedian(insar_dis[insar_flag] - gnss_dis[gnss_flag])\n",
     "\n",
-    "    ## plot figure\n",
+    "    ## Plot figure\n",
     "    if gnss_dis.size > 0 and np.any(~np.isnan(insar_dis)):\n",
     "        fig, ax = plt.subplots(figsize=(10, 3))\n",
     "        ax.axhline(color='grey',linestyle='dashed', linewidth=2)\n",

methods/transient/Transient_Requirement_Validation.ipynb

@@ -140,7 +140,7 @@
    },
    "outputs": [],
    "source": [
-    "# load packages\n",
+    "# Load packages\n",
     "import copy\n",
     "import glob\n",
     "import math\n",
@@ -589,7 +589,7 @@
     "    gnss_obj = gnss.get_gnss_class('UNR')(site = stn, data_dir = os.path.join(mintpy_dir,'GNSS'))\n",
     "    gnss_obj.open()\n",
     "        \n",
-    "    # count number of dates in time range\n",
+    "    # Count number of dates in time range\n",
     "    gnss_obj.read_displacement()\n",
     "    dates = gnss_obj.dates\n",
     "    for i in range(insar_displacement.shape[0]):\n",
@@ -601,17 +601,17 @@
     "        gnss_count = int(gnss_count[0])\n",
     "        #print(gnss_count)\n",
     "\n",
-    "        # select GNSS stations based on data completeness, here we hope to select stations with data frequency of 1 day and no interruption\n",
+    "        # Select GNSS stations based on data completeness, here we hope to select stations with data frequency of 1 day and no interruption\n",
     "        if range_days == gnss_count-1:\n",
-    "        #if start_date in dates and end_date in dates:\n",
+    "        # If start_date in dates and end_date in dates:\n",
     "            disp_gnss_time_series,disp_gnss_time_series_std,site_latlon = gnss_obj.get_los_displacement(os.path.join(mintpy_dir,'inputs/geometryGeo.h5'),\n",
     "                                                                                                            start_date=start_date.strftime('%Y%m%d'),\n",
     "                                                                                                            end_date=end_date.strftime('%Y%m%d'))[1:4]\n",
     "            x_value = round((site_latlon[1] - W)/lon_step)\n",
     "            y_value = round((site_latlon[0] - N)/lat_step)\n",
     "\n",
-    "            #displacement from insar observation in the gnss station, averaged\n",
-    "            #Caution: If you expand the radius parameter farther than the bounding grid it will break. \n",
+    "            # Displacement from insar observation in the gnss station, averaged\n",
+    "            # Caution: If you expand the radius parameter farther than the bounding grid it will break. \n",
     "            disp_insar = insar_displacement[i,\n",
     "                                            y_value-pixel_radius:y_value+pixel_radius, \n",
     "                                            x_value-pixel_radius:x_value+pixel_radius]\n",
@@ -749,7 +749,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# reference GNSS stations to GNSS reference site\n",
+    "# Reference GNSS stations to GNSS reference site\n",
     "for i in displacement.index.get_level_values(0).unique():\n",
     "    gnss_ref_site_name = random.choice(displacement.loc[i].index.unique())\n",
     "    displacement.loc[i,'gnss_disp'] = displacement.loc[i,'gnss_disp'].values - displacement.loc[(i,gnss_ref_site_name),'gnss_disp']\n",
@@ -1020,7 +1020,8 @@
    "outputs": [],
    "source": [
     "ratio = n_pass/n_all\n",
-    "thresthod = 0.683 \n",
+    "thresthod = 0.683\n",
+    "\n",
     "#The assumed nature of Gaussian distribution gives a probability of 0.683 of being within one standard deviation.\n",
     "success_or_fail = ratio>thresthod"
    ]
@@ -1654,7 +1655,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.12.8"
   },
   "toc-autonumbering": false,
   "toc-showcode": false,