Change default cmap for wrapped phase from insar to SCM.romaO

LiCSBAS_lib/LiCSBAS_loop_lib.py

@@ -8,6 +8,8 @@
 =========
 Changelog
 =========
+v1.5.1 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.5 20201006 Yu Morishita, GSI
  - Update make_loop_png
 v1.4 20200828 Yu Morishita, GSI
@@ -27,7 +29,6 @@
 import numpy as np
 import SCM
 import LiCSBAS_io_lib as io_lib
-import LiCSBAS_tools_lib as tools_lib
 
 os.environ['QT_QPA_PLATFORM']='offscreen'
 import warnings
@@ -120,12 +121,10 @@ def identify_bad_ifg(bad_ifg_cand, good_ifg):
 
 #%% 
 def make_loop_png(unw12, unw23, unw13, loop_ph, png, titles4, cycle):
-    ### Load color map for InSAR
-    cdict = tools_lib.cmap_insar()
-    plt.register_cmap(cmap=mpl.colors.LinearSegmentedColormap('insar', cdict))
-    plt.rcParams['axes.titlesize'] = 10
+    cmap_wrap = SCM.romaO
 
     ### Settings    
+    plt.rcParams['axes.titlesize'] = 10
     data = [unw12, unw23, unw13]
 
     length, width = unw12.shape
@@ -145,7 +144,7 @@ def make_loop_png(unw12, unw23, unw13, loop_ph, png, titles4, cycle):
     for i in range(3):
         data_wrapped = np.angle(np.exp(1j*(data[i]/cycle))*cycle)
         ax = fig.add_subplot(2, 2, i+1) #index start from 1
-        ax.imshow(data_wrapped, vmin=-np.pi, vmax=+np.pi, cmap='insar', interpolation='nearest')
+        ax.imshow(data_wrapped, vmin=-np.pi, vmax=+np.pi, cmap=cmap_wrap, interpolation='nearest')
         ax.set_title('{}'.format(titles4[i]))
         ax.set_xticklabels([])
         ax.set_yticklabels([])

LiCSBAS_lib/LiCSBAS_tools_lib.py

@@ -82,7 +82,7 @@ def comp_size_time(file_remote, file_local):
 #%%
 def cmap_insar():
     """
-    How to use cmap_insar:
+    How to use cmap_insar (GAMMA standard rainbow cmap):
         import matplotlib as mpl
         from matplotlib import pyplot as plt
         cdict = cmap_insar()

bin/LiCSBAS02_ml_prep.py

@@ -1,10 +1,7 @@
 #!/usr/bin/env python3
 """
-v1.7.3 202011118 Yu Morishita, GSI
+v1.7.4 202011119 Yu Morishita, GSI
 
-========
-Overview
-========
 This script converts GeoTIFF files of unw and cc to float32 and uint8 format, respectively, for further time series analysis, and also downsamples (multilooks) data if specified. Existing files are not re-created to save time, i.e., only the newly available data will be processed.
 
 ====================
@@ -48,6 +45,8 @@
 """
 #%% Change log
 '''
+v1.7.4 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.7.3 20201118 Yu Morishita, GSI
  - Again Bug fix of multiprocessing
 v1.7.2 20201116 Yu Morishita, GSI
@@ -82,7 +81,6 @@
 #%% Import
 import getopt
 import os
-import re
 import sys
 import time
 import shutil
@@ -91,6 +89,7 @@
 import numpy as np
 import subprocess as subp
 import multiprocessing as multi
+import SCM
 import LiCSBAS_io_lib as io_lib
 import LiCSBAS_tools_lib as tools_lib
 import LiCSBAS_plot_lib as plot_lib
@@ -109,12 +108,12 @@ def main(argv=None):
         argv = sys.argv
 
     start = time.time()
-    ver="1.7.3"; date=202011118; author="Y. Morishita"
+    ver="1.7.4"; date=20201119; author="Y. Morishita"
     print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True)
     print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True)
 
     ### For parallel processing
-    global ifgdates2, geocdir, outdir, nlook, n_valid_thre, cycle, cmap
+    global ifgdates2, geocdir, outdir, nlook, n_valid_thre, cycle, cmap_wrap
 
 
     #%% Set default
@@ -127,7 +126,7 @@ def main(argv=None):
     except:
         n_para = multi.cpu_count()
 
-    cmap = 'insar'
+    cmap_wrap = SCM.romaO 
     cycle = 3
     n_valid_thre = 0.5
     q = multi.get_context('fork')
@@ -444,7 +443,7 @@ def convert_wrapper(i):
 
     ### Make png
     unwpngfile = os.path.join(ifgdir1, ifgd+'.unw.png')
-    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), unwpngfile, cmap, ifgd+'.unw', vmin=-np.pi, vmax=np.pi, cbar=False)
+    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), unwpngfile, cmap_wrap, ifgd+'.unw', vmin=-np.pi, vmax=np.pi, cbar=False)
 
     return 0
 

bin/LiCSBAS03op_GACOS.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-v1.5.4 20201119 Yu Morishita, GSI
+v1.5.5 20201119 Yu Morishita, GSI
 
 This script applies a tropospheric correction to unw data using GACOS data. GACOS data may be automatically downloaded from COMET-LiCS web at step01 (if available), or could be externally obtained by requesting on a GACOS web (http://www.gacos.net/).
 If you request the GACOS data through the GACOS web, the dates and time of interest can be found in baselines and slc.mli.par, respectively. These are also available on the COMET-LiCS web portal. Once the GACOS data are ready, download the tar.gz, uncompress it, and put into GACOS dir. 
@@ -49,6 +49,8 @@
 """
 #%% Change log
 '''
+v1.5.5 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.5.4 20201119 Yu Morishita, GSI
  - New GACOS format (ztd.tif) available
 v1.5.3 20201118 Yu Morishita, GSI
@@ -85,6 +87,7 @@
 import numpy as np
 from osgeo import gdal
 import multiprocessing as multi
+import SCM
 import LiCSBAS_io_lib as io_lib
 import LiCSBAS_tools_lib as tools_lib
 import LiCSBAS_plot_lib as plot_lib
@@ -159,14 +162,14 @@ def main(argv=None):
         argv = sys.argv
 
     start = time.time()
-    ver="1.5.4"; date=20201119; author="Y. Morishita"
+    ver="1.5.5"; date=20201119; author="Y. Morishita"
     print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True)
     print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True)
 
     ### For parallel processing
     global imdates2, gacosdir, outputBounds, width_geo, length_geo, resampleAlg,\
         sltddir, LOSu, m2r_coef, fillholeflag, ifgdates2,\
-        in_dir, out_dir, length_unw, width_unw, cycle
+        in_dir, out_dir, length_unw, width_unw, cycle, cmap_wrap
 
 
     #%% Set default
@@ -181,7 +184,7 @@ def main(argv=None):
         n_para = multi.cpu_count()
 
     q = multi.get_context('fork')
-
+    cmap_wrap = SCM.romaO
 
     #%% Read options
     try:
@@ -532,12 +535,12 @@ def correct_wrapper(i):
     data3 = [np.angle(np.exp(1j*(data/cycle))*cycle) for data in [unw, unw_cor, dsltd]]
     title3 = ['unw_org (STD: {:.1f} rad)'.format(std_unw), 'unw_cor (STD: {:.1f} rad)'.format(std_unwcor), 'dsltd ({:.1f}% reduced)'.format(rate)]
     pngfile = os.path.join(out_dir1, ifgd+'.gacos.png')
-    plot_lib.make_3im_png(data3, pngfile, 'insar', title3, vmin=-np.pi, vmax=np.pi, cbar=False)
+    plot_lib.make_3im_png(data3, pngfile, cmap_wrap, title3, vmin=-np.pi, vmax=np.pi, cbar=False)
 
     ## Output png for corrected unw
     pngfile = os.path.join(out_dir1, ifgd+'.unw.png')
     title = '{} ({}pi/cycle)'.format(ifgd, cycle*2)
-    plot_lib.make_im_png(np.angle(np.exp(1j*unw_cor/cycle)*cycle), pngfile, 'insar', title, -np.pi, np.pi, cbar=False)
+    plot_lib.make_im_png(np.angle(np.exp(1j*unw_cor/cycle)*cycle), pngfile, cmap_wrap, title, -np.pi, np.pi, cbar=False)
 
     return 2, [ifgd, std_unw, std_unwcor, rate]
 

bin/LiCSBAS04op_mask_unw.py

@@ -1,10 +1,7 @@
 #!/usr/bin/env python3
 """
-v1.3.3 20201118 Yu Morishita, GSI
+v1.3.4 20201119 Yu Morishita, GSI
 
-========
-Overview
-========
 This script masks specified areas or low coherence areas in the unw data. The masking is effective when the unw data include areas which have many unwrapping errors and are not of interest, and can improve the result of Step 1-2 (loop closure). Existing files are not re-created to save time, i.e., only the newly available data will be processed. This step is optional.
 
 ===============
@@ -42,6 +39,8 @@
 """
 #%% Change log
 '''
+v1.3.4 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.3.3 20201118 Yu Morishita, GSI
  - Again Bug fix of multiprocessing
 v1.3.2 20201116 Yu Morishita, GSI
@@ -67,6 +66,7 @@
 import time
 import numpy as np
 import multiprocessing as multi
+import SCM
 import LiCSBAS_io_lib as io_lib
 import LiCSBAS_tools_lib as tools_lib
 import LiCSBAS_plot_lib as plot_lib
@@ -84,12 +84,12 @@ def main(argv=None):
         argv = sys.argv
 
     start = time.time()
-    ver="1.3.3"; date=20201118; author="Y. Morishita"
+    ver="1.3.4"; date=20201119; author="Y. Morishita"
     print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True)
     print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True)
 
     ### For paralell processing
-    global ifgdates2, in_dir, out_dir, length, width, bool_mask, cycle
+    global ifgdates2, in_dir, out_dir, length, width, bool_mask, cycle, cmap_wrap
 
 
     #%% Set default
@@ -104,6 +104,7 @@ def main(argv=None):
         n_para = multi.cpu_count()
 
     cmap_noise = 'viridis'
+    cmap_wrap = SCM.romaO
     q = multi.get_context('fork')
 
 
@@ -314,7 +315,7 @@ def mask_wrapper(ifgix):
     ## Output png for masked unw
     pngfile = os.path.join(out_dir1, ifgd+'.unw.png')
     title = '{} ({}pi/cycle)'.format(ifgd, cycle*2)
-    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), pngfile, 'insar', title, -np.pi, np.pi, cbar=False)
+    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), pngfile, cmap_wrap, title, -np.pi, np.pi, cbar=False)
 
 
 #%% main

bin/LiCSBAS05op_clip_unw.py

@@ -1,10 +1,7 @@
 #!/usr/bin/env python3
 """
-v1.2.3 20201118 Yu Morishita, GSI
+v1.2.4 20201119 Yu Morishita, GSI
 
-========
-Overview
-========
 This script clips a specified rectangular area of interest from unw and cc data. The clipping can make the data size smaller and processing faster, and improve the result of Step 1-2 (loop closure). Existing files are not re-created to save time, i.e., only the newly available data will be processed. This step is optional.
 
 ===============
@@ -42,6 +39,8 @@
 """
 #%% Change log
 '''
+v1.2.4 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.2.3 20201118 Yu Morishita, GSI
  - Again Bug fix of multiprocessing
 v1.2.2 20201116 Yu Morishita, GSI
@@ -67,6 +66,7 @@
 import time
 import numpy as np
 import multiprocessing as multi
+import SCM
 import LiCSBAS_io_lib as io_lib
 import LiCSBAS_tools_lib as tools_lib
 import LiCSBAS_plot_lib as plot_lib
@@ -85,12 +85,12 @@ def main(argv=None):
         argv = sys.argv
 
     start = time.time()
-    ver="1.2.3"; date=20201118; author="Y. Morishita"
+    ver="1.2.4"; date=20201119; author="Y. Morishita"
     print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True)
     print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True)
 
     ### For parallel processing
-    global ifgdates2, in_dir, out_dir, length, width, x1, x2, y1, y2,cycle
+    global ifgdates2, in_dir, out_dir, length, width, x1, x2, y1, y2,cycle, cmap_wrap
 
 
     #%% Set default
@@ -104,6 +104,7 @@ def main(argv=None):
         n_para = multi.cpu_count()
 
     q = multi.get_context('fork')
+    cmap_wrap = SCM.romaO
 
 
     #%% Read options
@@ -333,7 +334,7 @@ def clip_wrapper(ifgix):
     ## Output png for corrected unw
     pngfile = os.path.join(out_dir1, ifgd+'.unw.png')
     title = '{} ({}pi/cycle)'.format(ifgd, cycle*2)
-    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), pngfile, 'insar', title, -np.pi, np.pi, cbar=False)
+    plot_lib.make_im_png(np.angle(np.exp(1j*unw/cycle)*cycle), pngfile, cmap_wrap, title, -np.pi, np.pi, cbar=False)
 
 
 #%% main

bin/LiCSBAS13_sb_inv.py

@@ -1,10 +1,7 @@
 #!/usr/bin/env python3
 """
-v1.4.5 20201118 Yu Morishita, GSI
+v1.4.6 20201119 Yu Morishita, GSI
 
-========
-Overview
-========
 This script inverts the SB network of unw to obtain the time series and velocity 
 using NSBAS (López-Quiroz et al., 2009; Doin et al., 2011) approach.
 A stable reference point is determined after the inversion. RMS of the time series
@@ -72,6 +69,8 @@
 """
 #%% Change log
 '''
+v1.4.6 20201119 Yu Morishita, GSI
+ - Change default cmap for wrapped phase from insar to SCM.romaO
 v1.4.5 20201118 Yu Morishita, GSI
  - Again Bug fix of multiprocessing
 v1.4.4 20201116 Yu Morishita, GSI
@@ -132,14 +131,14 @@ def main(argv=None):
         argv = sys.argv
 
     start = time.time()
-    ver="1.4.5"; date=20201118; author="Y. Morishita"
+    ver="1.4.6"; date=20201119; author="Y. Morishita"
     print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True)
     print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True)
 
     ## For parallel processing
     global n_para_gap, G, Aloop, unwpatch, imdates, incdir, ifgdir, length, width,\
         coef_r2m, ifgdates, ref_unw, cycle, keep_incfile, resdir, restxtfile, \
-        cmap_vel, wavelength
+        cmap_vel, cmap_wrap, wavelength
 
 
     #%% Set default
@@ -161,6 +160,7 @@ def main(argv=None):
     cmap_vel = SCM.roma.reversed()
     cmap_noise = 'viridis'
     cmap_noise_r = 'viridis_r'
+    cmap_wrap = SCM.romaO
     q = multi.get_context('fork')
 
 
@@ -827,7 +827,7 @@ def inc_png_wrapper(imx):
     data3 = [np.angle(np.exp(1j*(data/coef_r2m/cycle))*cycle) for data in [unw, inc, inc-unw]]
     title3 = ['Daisy-chain IFG ({}pi/cycle)'.format(cycle*2), 'Inverted ({}pi/cycle)'.format(cycle*2), 'Difference ({}pi/cycle)'.format(cycle*2)]
     pngfile = os.path.join(incdir, '{}.increment.png'.format(ifgd))
-    plot_lib.make_3im_png(data3, pngfile, 'insar', title3, vmin=-np.pi, vmax=np.pi, cbar=False)
+    plot_lib.make_3im_png(data3, pngfile, cmap_wrap, title3, vmin=-np.pi, vmax=np.pi, cbar=False)
 
     if not keep_incfile:
         os.remove(incfile)