Merge pull request #413 from johntruckenbrodt/bugfix/gamma_shellscript

gamma: shellscript improvements

Author: johntruckenbrodt

pyroSAR/gamma/auxil.py

@@ -285,6 +285,7 @@ class Namespace(object):
     >>> print(n.pix_geo)
     '/path/S1A__IW___A_20180829T170631_pix_geo'
     """
+    
     def __init__(self, directory, basename):
         self.__base = basename
         self.__outdir = directory
@@ -393,32 +394,40 @@ def par2hdr(parfile, hdrfile, modifications=None, nodata=None):
         hdr(items, hdrfile)
 
 
-def process(cmd, outdir=None, logfile=None, logpath=None,
-            inlist=None, void=True, shellscript=None):
+def process(
+        cmd: list[str],
+        outdir: str | None = None,
+        logfile: str | None = None,
+        logpath: str | None = None,
+        inlist: list[str] | None = None,
+        void: bool = True,
+        shellscript: str | None = None
+) -> tuple[str, str] | None:
     """
     wrapper function to execute GAMMA commands via module :mod:`subprocess`
 
     Parameters
     ----------
-    cmd: list[str]
-        the command line arguments
-    outdir: str
-        the directory to execute the command in
-    logfile: str
-        a file to write the command log to; overrides parameter logpath
-    logpath: str
-        a directory to write logfiles to; the file will be named {GAMMA command}.log, e.g. gc_map.log;
-        is overridden by parameter logfile
-    inlist: list
-        a list of values, which is passed as interactive inputs via stdin
-    void: bool
-        return the stdout and stderr messages?
-    shellscript: str
-        a file to write the GAMMA commands to in shell format
+    cmd:
+        The command line arguments.
+    outdir:
+        The directory to execute the command in. This directory is also set
+        as environment variable in `shellscript`.
+    logfile:
+        A file to write the command log to. Overrides parameter `logpath`.
+    logpath:
+        A directory to write logfiles to. The file will be named
+        {GAMMA command}.log, e.g. gc_map.log.
+        Overrides parameter `logfile`.
+    inlist:
+        A list of values, which is passed as interactive inputs via `stdin`.
+    void:
+        Return the `stdout` and `stderr` messages?
+    shellscript:
+        A file to write the GAMMA commands to in shell format.
 
     Returns
     -------
-    tuple of str or None
         the stdout and stderr messages if void is False, otherwise None
     """
     if logfile is not None:
@@ -435,17 +444,21 @@ def process(cmd, outdir=None, logfile=None, logpath=None,
         if inlist is not None:
             line += ' <<< $"{}"'.format('\n'.join([str(x) for x in inlist]) + '\n')
         with open(shellscript, 'r+') as sh:
+            content = sh.read()
+            sh.seek(0)
+            disclaimer = 'This script was created automatically by pyroSAR'
+            is_new = re.search(disclaimer, content) is None
+            if is_new:
+                ts = datetime.now().strftime('%a %b %d %H:%M:%S %Y')
+                sh.write(f'# {disclaimer} on {ts}\n\n')
+                sh.write('GAMMA_HOME={}\n\n'.format(gamma_home))
+                sh.write(content)
+            line = line.replace(gamma_home, '$GAMMA_HOME')
             if outdir is not None:
-                content = sh.read()
-                sh.seek(0)
-                is_new = re.search('this script was created automatically by pyroSAR', content) is None
-                if is_new:
-                    ts = datetime.now().strftime('%a %b %d %H:%M:%S %Y')
-                    sh.write('# this script was created automatically by pyroSAR on {}\n\n'.format(ts))
-                    sh.write('export base={}\n'.format(outdir))
-                    sh.write('export GAMMA_HOME={}\n\n'.format(gamma_home))
-                    sh.write(content)
-                line = line.replace(outdir, '$base').replace(gamma_home, '$GAMMA_HOME')
+                line = line.replace(outdir, '$OUTDIR')
+                outdirs = re.findall('OUTDIR=(.*)\n', content)
+                if len(outdirs) == 0 or outdir != outdirs[-1]:
+                    line = f"OUTDIR={outdir}\n\n{line}"
             sh.seek(0, 2)  # set pointer to the end of the file
             sh.write(line + '\n\n')
 

pyroSAR/gamma/dem.py

@@ -1,7 +1,7 @@
 ###############################################################################
 # preparation of DEM data for use in GAMMA
 
-# Copyright (c) 2014-2022, the pyroSAR Developers.
+# Copyright (c) 2014-2026, the pyroSAR Developers.
 
 # This file is part of the pyroSAR Project. It is subject to the
 # license terms in the LICENSE.txt file found in the top-level
@@ -299,30 +299,36 @@ def dem_autocreate(geometry, demType, outfile, buffer=None, t_srs=4326, tr=None,
         shutil.rmtree(tmpdir)
 
 
-def dem_import(src, dst, geoid=None, logpath=None, outdir=None):
+def dem_import(
+        src: str,
+        dst: str,
+        geoid: str | None = None,
+        logpath: str | None = None,
+        outdir: str | None = None,
+        shellscript: str | None = None
+) -> None:
     """
-    convert an existing DEM in GDAL-readable format to GAMMA format including optional geoid-ellipsoid conversion.
+    convert an existing DEM in GDAL-readable format to GAMMA
+    format including optional geoid-ellipsoid conversion.
     
     Parameters
     ----------
-    src: str
+    src:
         the input DEM
-    dst: str
+    dst:
         the output DEM
-    geoid: str or None
+    geoid:
         the geoid height reference of `src`; supported options:
         
         - 'EGM96'
         - 'EGM2008'
         - None: assume WGS84 ellipsoid heights and do not convert heights
-    logpath: str or None
+    logpath:
         a directory to write logfiles to
-    outdir: str or None
+    outdir:
         the directory to execute the command in
-
-    Returns
-    -------
-
+    shellscript:
+        a file to write the GAMMA commands to in shell format
     """
     with raster.Raster(src) as ras:
         epsg = ras.epsg
@@ -349,25 +355,30 @@ def dem_import(src, dst, geoid=None, logpath=None, outdir=None):
                       gflg=gflg,
                       geoid='-',
                       logpath=logpath,
-                      outdir=outdir)
+                      outdir=outdir,
+                      shellscript=shellscript)
     else:
         # new approach enabling an arbitrary target CRS EPSG code
         diff.create_dem_par(DEM_par=dst_base + '.par',
                             inlist=[''] * 9,
-                            EPSG=epsg)
+                            EPSG=epsg,
+                            logpath=logpath,
+                            outdir=outdir,
+                            shellscript=shellscript)
         dem_import_pars = {'input_DEM': src,
                            'DEM': dst,
                            'DEM_par': dst_base + '.par',
                            'logpath': logpath,
-                           'outdir': outdir}
+                           'outdir': outdir,
+                           'shellscript': shellscript}
         if gflg == 2:
             home = ExamineGamma().home
             if geoid == 'EGM96':
                 geoid_file = os.path.join(home, 'DIFF', 'scripts', 'egm96.dem')
             elif geoid == 'EGM2008':
                 geoid_file = os.path.join(home, 'DIFF', 'scripts', 'egm2008-5.dem')
             else:
-                raise RuntimeError('conversion of {} geoid is not supported by GAMMA'.format(geoid))
+                raise RuntimeError(f"conversion of '{geoid}' geoid is not supported by GAMMA")
             dem_import_pars['geoid'] = geoid_file
             dem_import_pars['geoid_par'] = geoid_file + '_par'
 

pyroSAR/gamma/error.py

@@ -81,7 +81,7 @@ def gammaErrorHandler(returncode: int, out: str, err: str) -> None:
                     else:
                         return
         else:
-            err_out = f'failed with return code {returncode}'
+            err_out = f'{err}\nfailed with return code {returncode}'
             if returncode < 0:
                 # handle signal kills like SIGSEGV (segmentation fault)
                 sig = signal.Signals(-returncode)