attempt to (manually) merge (#31)

* 1 reload patches (#6) * Add option to restart processing * Update .gitignore * Add some testing print statements * Add xarray * Allow storing and loading of patches * 3 aggressive nullification (#7) * Add reset nulls script * Add aggressive nullifying, nullmask and null both * Add remove noloops script * Add backup unnulled data option * 2 add in polymask option (#8) * Add def polymask * Add polyclipping, using inverted polymask * 4 coherence masking (#9) * Add option to plot coherence * Update with qi's networks, and log scales ofr coherence * And poly mask and coherence masking * supervised autocorrection correcting some of typos etc. * trying fix permissions from windows * Allow polyclips and range_str to be used * Add print statement in case no patches are found * 12 clip05 bugs (#13) * Add check for -r, -g or -p * Add rangestr for polyclip * Set coherence to 0 rather than NaN * Invert bool mask * Always use a bool mask * 12 clip05 bugs (#14) * Add check for -r, -g or -p * Add rangestr for polyclip * Set coherence to 0 rather than NaN * Invert bool mask * Always use a bool mask * Drop try/finally statements when clipping * Update LiCSBAS13_sb_inv.py fixed bug (cumfile definition) * bug fix LiCSBAS01 * regular update * Unwrapping correction * cum2vel_weighted * 130_sb_inv to allow for user defined ifg list 133 to recalculate stats and make final cum.h5 * make a cum from epoch data * densify network from a given ifg list by adding a target number of new ifgs * choose reference from 4 proxies * remove reference effect * graph theory and some io changes * added functional LiCSBAS02to05 * regular update * updated permissions * updated reqs (networkx) * Update environment.yml * added snaphu to binder * set OMP_NUM_THREADS to 1 * Update LiCSBAS12_loop_closure.py * Update environment.yml removed faulty pip install of licsar_extra... keep it manually then * Update LiCSBAS_meta.py bug fix * Update postBuild tutorial: prepare also preprocessed data (TS folder) * Update postBuild * Update postBuild * Update licsbas_tutorial.ipynb minor edit * Update licsbas_tutorial.ipynb --------- Co-authored-by: JackDMcGrath <[email protected]> Co-authored-by: laz048 <[email protected]> Co-authored-by: Lin Shen Co-authored-by: qi-ou <[email protected]> Co-authored-by: qi-ou <[email protected]>
comet-licsar · Sep 6, 2023 · b866a1a · b866a1a
1 parent c5b5db5
commit b866a1a
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Showing 37 changed files with 6,081 additions and 978 deletions.
diff --git a/.gitignore b/.gitignore
@@ -108,3 +108,5 @@ venv.bak/
 .idea/modules.xml
 .idea/vcs.xml
 .idea/workspace.xml
+
+.vscode/
diff --git a/LiCSBAS.yml b/LiCSBAS.yml
@@ -14,3 +14,4 @@ dependencies:
   - shapely
   - statsmodels
   - colorcet
+  - xarray
diff --git a/LiCSBAS_lib/LiCSBAS_io_lib.py b/LiCSBAS_lib/LiCSBAS_io_lib.py
@@ -53,6 +53,9 @@ def make_geotiff(data, latn_p, lonw_p, dlat, dlon, outfile, compress_option, nod
         dtype = gdal.GDT_Float32
     elif data.dtype == np.uint8:
         dtype = gdal.GDT_Byte
+    else:
+        print('error with the data format - neither float nor int')
+        return
 
     driver = gdal.GetDriverByName('GTiff')
     outRaster = driver.Create(outfile, width, length, 1, dtype, options=compress_option)
@@ -144,6 +147,8 @@ def read_bperp_file(bperp_file, imdates):
     ### Determine type of bperp_file; old or not
     with open(bperp_file) as f:
         line = f.readline().split() #list
+        if not line[0].startswith("2"):
+            line = f.readline().split()  # find first line that starts with '2'
 
     if len(line) == 4: ## new format
         bperp_dict[line[0]] = '0.00' ## single prime. unnecessary?
@@ -209,15 +214,15 @@ def read_ifg_list(ifg_listfile):
     ifgdates = []
     f = open(ifg_listfile)
     line = f.readline()
+
     while line:
-        ifgd = line.split()[0]
-        if ifgd == "#":
+        if line[0] == "2":
+            ifgd = line.split()[0]
+            ifgdates.append(str(ifgd))
             line = f.readline()
-            continue # Comment
         else:
-            ifgdates.append(ifgd)
             line = f.readline()
-    f.close()
+            continue
 
     return ifgdates
 
@@ -237,3 +242,24 @@ def get_param_par(mlipar, field):
     value = subp.check_output(['grep', field,mlipar]).decode().split()[1].strip()
     return value
 
+
+#%%
+def read_residual_file(resid_file):
+    """
+    # RMS of residual (in number of 2pi)
+    20141018_20141205  0.07
+    ...
+    20220720_20220801  0.06
+    RMS_mode:  0.05
+    RMS_median:  0.10
+    RMS_mean:  0.13
+    RMS_thresh:  0.20
+    """
+    ifg_list = []
+    residual_list = []
+    with open(resid_file) as f:
+        for l in f:
+            if l.startswith("2"):
+                ifg_list.append(l.split()[0])
+                residual_list.append(float(l.split()[1]))
+    return ifg_list, residual_list
diff --git a/LiCSBAS_lib/LiCSBAS_meta.py b/LiCSBAS_lib/LiCSBAS_meta.py
@@ -0,0 +1,9 @@
+# version control
+ver='1.14.2 (dev)'
+date='2023-06-28'
+author="Dr. Yu Morishita and COMET dev team (ML,QO,JM,LS,..)"
+
+# setting number of threads to small number (e.g. 1), as the multiprocessing appears slow otherwise
+# solution found by Richard Rigby, Uni of Leeds
+import os
+os.environ["OMP_NUM_THREADS"] = '1'