support PIXEL/ALOS1 .gz files

uncompressFile.py: support multiple sub-layers of folders uncompressing

prepRawALOS.py:
1. add get_ALOS_ALP_name() to support the compressed ALOS file that is not named with "ALP*", such as the ones from PIXEL
2. remove duplicated inputDir, outputDir and rmfile, as they are in the Namespace inps object already.
3. move the inputDir and outputDir abspath from main() to cmdLineParse()
4. basic formating adjustment

.gitignore

@@ -1,6 +1,7 @@
 *.pyc
 *~
 *.swp
+*.DS_Store
 __pycache__
 .sconf_temp
 .sconsign.dblite

contrib/stack/stripmapStack/prepRawALOS.py

@@ -1,25 +1,32 @@
 #!/usr/bin/env python3
 # David Bekaert
+
+
 import os
 import glob
 import argparse
-from uncompressFile import uncompressfile
 import shutil
+import tarfile
+import zipfile
+from uncompressFile import uncompressfile
+
 
 def createParser():
     '''
     Create command line parser.
     '''
 
-    parser = argparse.ArgumentParser(description='Prepare ALOS raw processing (unzip/untar files, organize in date folders, generate script to unpack into isce formats).')
+    parser = argparse.ArgumentParser(description='Prepare ALOS raw processing (unzip/untar files, '
-    parser.add_argument('-i', '--input', dest='input', type=str, required=True,
+                                     'organize in date folders, generate script to unpack into isce formats).')
+    parser.add_argument('-i', '--input', dest='inputDir', type=str, required=True,
             help='directory with the raw data')
     parser.add_argument('-rmfile', '--rmfile', dest='rmfile',action='store_true', default=False,
-            help='Optional: remove zip/tar/compressed files after unpacking into date structure (default is to keep in archive fo  lder)')
+            help='Optional: remove zip/tar/compressed files after unpacking into date structure '
-    parser.add_argument('-o', '--output', dest='output', type=str, required=False,
+                 '(default is to keep in archive fo  lder)')
+    parser.add_argument('-o', '--output', dest='outputDir', type=str, required=False,
             help='output directory where data needs to be unpacked into isce format (for script generation).')
-    parser.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='source ~/.bash_profile;'
+    parser.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='source ~/.bash_profile;',
-       , help='text command to be added to the beginning of each line of the run files. Default: source ~/.bash_profile;')
+            help='text command to be added to the beginning of each line of the run files. Default: source ~/.bash_profile;')
     return parser
 
 
@@ -29,7 +36,15 @@ def cmdLineParse(iargs=None):
     '''
 
     parser = createParser()
-    return parser.parse_args(args = iargs)
+    inps = parser.parse_args(args = iargs)
+
+    # parsing required inputs
+    inps.inputDir = os.path.abspath(inps.inputDir)
+    # parsing optional inputs
+    if inps.outputDir:
+        inps.outputDir = os.path.abspath(inps.outputDir)
+    return inps
+
 
 def get_Date(ALOSfolder):
 
@@ -56,46 +71,60 @@ def get_Date(ALOSfolder):
     acquisitionDate = 'FAIL'
     return successflag, acquisitionDate
 
+
+def get_ALOS_ALP_name(infile):
+    """Get the ALPSRP075780620 name from compress file in various format."""
+    outname = None
+    fbase = os.path.basename(infile)
+    if fbase.startswith("ALP"):
+        outname = fbase.split("-")[0]
+    else:
+        fext = os.path.splitext(infile)[1]
+        if fext in ['.tar', '.gz']:
+            with tarfile.open(infile, 'r') as tar:
+                file_list = tar.getnames()
+        elif fext in ['.zip']:
+            with zipfile.ZipFile(infile, 'r') as z:
+                file_list = z.namelist()
+        else:
+            raise ValueError('unrecognized file extension: {}'.format(fext))
+        led_file = [i for i in file_list if 'LED' in i][0]
+        led_file = os.path.basename(led_file)
+        outname = [i for i in led_file.split("-") if 'ALP' in i][0]
+    return outname
+
+
 def main(iargs=None):
     '''
     The main driver.
     '''
 
     inps = cmdLineParse(iargs)
-    # parsing required inputs
-    inputDir = os.path.abspath(inps.input)
-    # parsing optional inputs
-    if inps.output:
-        outputDir = os.path.abspath(inps.output)
-    else:
-        outputDir = None
-    rmfile = inps.rmfile
 
     # filename of the runfile
     run_unPack = 'run_unPackALOS'   
 
     # loop over the different folder, ALOS zip/tar files and unzip them, make the names consistent
-    ALOS_extensions = (os.path.join(inputDir, 'ALP*.zip'),os.path.join(inputDir, 'ALP*.tar'),os.path.join(inputDir, 'ALP*.gz'))
+    ALOS_extensions = (os.path.join(inps.inputDir, '*.zip'),
+                       os.path.join(inps.inputDir, '*.tar'),
+                       os.path.join(inps.inputDir, '*.gz'))
     for ALOS_extension in ALOS_extensions:
+        # loop over zip/tar files
         ALOS_filesfolders = glob.glob(ALOS_extension)
         for ALOS_infilefolder in ALOS_filesfolders:
             ## the path to the folder/zip
             workdir = os.path.dirname(ALOS_infilefolder)
 
             ## get the output name folder without any extensions
-            temp = os.path.basename(ALOS_infilefolder)
+            ALOS_outfolder = get_ALOS_ALP_name(ALOS_infilefolder)
-            # trim the extensions and keep only very first part
-            parts = temp.split(".")
-            parts = parts[0].split('-')
-            ALOS_outfolder = parts[0]
             # add the path back in
-            ALOS_outfolder = os.path.join(workdir,ALOS_outfolder)
+            ALOS_outfolder = os.path.join(workdir, ALOS_outfolder)
 
             # loop over two cases (either file or folder): 
             ### this is a file, try to unzip/untar it
             if os.path.isfile(ALOS_infilefolder):
                 # unzip the file in the outfolder
-                successflag_unzip = uncompressfile(ALOS_infilefolder,ALOS_outfolder)
+                successflag_unzip = uncompressfile(ALOS_infilefolder, ALOS_outfolder)
 
                 # put failed files in a seperate directory
                 if not successflag_unzip:
@@ -104,7 +133,7 @@ def main(iargs=None):
                     os.rename(ALOS_infilefolder,os.path.join(workdir,'FAILED_FILES','.'))
                 else:
                     # check if file needs to be removed or put in archive folder
-                    if rmfile:
+                    if inps.rmfile:
                         os.remove(ALOS_infilefolder)
                         print('Deleting: ' + ALOS_infilefolder)
                     else:
@@ -116,9 +145,10 @@ def main(iargs=None):
 
         # loop over the different ALOS folders and make sure the folder names are consistent.
         # this step is not needed unless the user has manually unzipped data before.
-        ALOS_folders = glob.glob(os.path.join(inputDir, 'ALP*'))
+        ALOS_folders = glob.glob(os.path.join(inps.inputDir, 'ALP*'))
         for ALOS_folder in ALOS_folders:
-            # in case the user has already unzipped some files, make sure they are unzipped similar like the uncompressfile code
+            # in case the user has already unzipped some files
+            # make sure they are unzipped similar like the uncompressfile code
             temp = os.path.basename(ALOS_folder)
             parts = temp.split(".")
             parts = parts[0].split('-')
@@ -134,7 +164,7 @@ def main(iargs=None):
 
 
     # loop over the different ALOS folders and organize in date folders
-    ALOS_folders = glob.glob(os.path.join(inputDir, 'ALP*'))                        
+    ALOS_folders = glob.glob(os.path.join(inps.inputDir, 'ALP*'))                        
     for ALOS_folder in ALOS_folders:
         # get the date
         successflag, imgDate = get_Date(ALOS_folder)       
@@ -160,14 +190,14 @@ def main(iargs=None):
         
 
     # now generate the unpacking script for all the date dirs
-    dateDirs = glob.glob(os.path.join(inputDir,'2*'))
+    dateDirs = glob.glob(os.path.join(inps.inputDir,'2*'))
-    if outputDir is not None:
+    if inps.outputDir is not None:
         f = open(run_unPack,'w')
         for dataDir in dateDirs:
             AlosFiles = glob.glob(os.path.join(dataDir, 'ALP*'))
             if len(AlosFiles)>0:
                 acquisitionDate = os.path.basename(dataDir)
-                slcDir = os.path.join(outputDir, acquisitionDate)
+                slcDir = os.path.join(inps.outputDir, acquisitionDate)
                 if not os.path.exists(slcDir):
                     os.makedirs(slcDir)     
                 cmd = 'unpackFrame_ALOS_raw.py -i ' + os.path.abspath(dataDir) + ' -o ' + slcDir      
@@ -179,9 +209,9 @@ def main(iargs=None):
                 print (cmd)
                 f.write(inps.text_cmd + cmd+'\n')
         f.close()
+    return
+
 
 if __name__ == '__main__':
 
     main()
-
-

contrib/stack/stripmapStack/uncompressFile.py

@@ -2,12 +2,14 @@
 
 # David Bekaert
 
-import zipfile
+
 import os
 import glob
 import argparse
-import tarfile
 import shutil
+import tarfile
+import zipfile
+
 
 def createParser():
     '''
@@ -50,6 +52,8 @@ def main(iargs=None):
         print('Done')
     elif completeFlag == False:
         print('Failed')
+    return
+
 
 def uncompressfile(inputFile,outputDir):
     
@@ -105,7 +109,7 @@ def uncompressfile(inputFile,outputDir):
 
             # Check if the data is unpacked in its own folder
             folderfiles = glob.glob(os.path.join(outputDir,'*'))
-            if len(folderfiles)==1:
+            while len(folderfiles)==1:
                 # get the sub-folder name only
                 tempdir = os.path.basename(folderfiles[0])
                 if os.path.isdir(folderfiles[0]):
@@ -114,7 +118,9 @@ def uncompressfile(inputFile,outputDir):
                     os.rename(folderfiles[0],tempdir2)
                     os.rmdir(outputDir)
                     os.rename(tempdir2,outputDir)
+                folderfiles = glob.glob(os.path.join(outputDir,'*'))
             return completeFlag
+
     elif extension == '.tar' or extension == '.gz':
         TAR = tarfile.open(inputFile)
 
@@ -124,17 +130,18 @@ def uncompressfile(inputFile,outputDir):
             TAR.close()
             completeFlag = True
 
-            # Check if the data is unpacked in its own folder
+            # Check if the data is unpacked in its own folder or its sub-folders
             folderfiles = glob.glob(os.path.join(outputDir,'*'))
-            if len(folderfiles)==1:
+            while len(folderfiles) == 1:
                 # get the sub-folder name only
                 tempdir = os.path.basename(folderfiles[0])
                 if os.path.isdir(folderfiles[0]):
                     # it seems there is a subfolder, will copy the content in the parent
-                    tempdir2=os.path.join(workdir,tempdir + '.temp')                                                                                
+                    tempdir2 = os.path.join(workdir, tempdir + '.temp')
                     os.rename(folderfiles[0],tempdir2)
                     os.rmdir(outputDir)
                     os.rename(tempdir2,outputDir)
+                folderfiles = glob.glob(os.path.join(outputDir,'*'))
             return completeFlag
         except:
             print('Tar file seems to be corrupted, abord...')