Feature/qc outdir

rawtools/cli.py

@@ -86,18 +86,31 @@ def raw_nsihdr():
 
 def raw_qc():
     """Quality control tools"""
-    description="Check the quality of a .RAW volume by extracting a slice or generating a projection. Requires a .RAW and .DAT for each volume."
-
-    parser = argparse.ArgumentParser(description=description, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument("-V", "--version", action="version", version=f'%(prog)s {__version__}')
-    parser.add_argument("-v", "--verbose", action="store_true", help="Increase output verbosity")
-    parser.add_argument("-f", "--force", action="store_true", default=False, help="Force file creation. Overwrite any existing files.")
-    parser.add_argument("--si", action="store_true", default=False, help="Print human readable sizes (e.g., 1 K, 234 M, 2 G)")
-    parser.add_argument("-p", "--projection", action="store", nargs='+', help="Generate projection using maximum values for each slice. Available options: [ 'top', 'side' ].")
-    parser.add_argument("--scale", dest="step", const=100, action="store", nargs='?', default=argparse.SUPPRESS, type=int, help="Add scale on left side of a side projection. Step is the number of slices between each label. (default: 100)")
-    parser.add_argument("-s", "--slice", dest='index', const=True, nargs='?', type=int, default=argparse.SUPPRESS, help="Extract a slice from volume's side view. (default: floor(x/2))")
-    parser.add_argument("--font-size", dest="font_size", action="store", type=int, default=24, help="Font size of labels of scale.")
-    parser.add_argument("path", metavar='PATH', type=str, nargs='+', help='Filepath to a .RAW or path to a directory that contains .RAW files.')
+    description = "Check the quality of a .RAW volume by extracting a slice or generating a projection. Requires a .RAW and .DAT for each volume."
+
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("-V", "--version", action="version",
+                        version=f'%(prog)s {__version__}')
+    parser.add_argument("-v", "--verbose", action="store_true",
+                        help="Increase output verbosity")
+    parser.add_argument("-f", "--force", action="store_true", default=False,
+                        help="Force file creation. Overwrite any existing files.")
+    parser.add_argument("--si", action="store_true", default=False,
+                        help="Print human readable sizes (e.g., 1 K, 234 M, 2 G)")
+    parser.add_argument("-n", '--dry-run', dest='dryrun', action="store_true",
+                        help="Perform a trial run. Do not create image files, but logs will be updated.")
+    parser.add_argument("-p", "--projection", action="store", nargs='+',
+                        help="Generate projection using maximum values for each slice. Available options: [ 'top', 'side' ].")
+    parser.add_argument("--scale", dest="step", const=100, action="store", nargs='?', default=argparse.SUPPRESS, type=int,
+                        help="Add scale on left side of a side projection. Step is the number of slices between each label. (default: 100)")
+    parser.add_argument("-s", "--slice", dest='index', const=True, nargs='?', type=int,
+                        default=argparse.SUPPRESS, help="Extract a slice from volume's side view. (default: floor(x/2))")
+    parser.add_argument("--font-size", dest="font_size", action="store",
+                        type=int, default=24, help="Font size of labels of scale.")
+    parser.add_argument("-o", "--outdir", action="store", help="Output folder to store all generated files. If not provided, each file will be placed in the folder of the source data.")
+    parser.add_argument("path", metavar='PATH', type=str, nargs='+',
+                        help='Filepath to a .RAW or path to a directory that contains .RAW files.')
     args = parser.parse_args()
 
     args.module_name = 'qc'

rawtools/log.py

@@ -9,43 +9,46 @@
 
 
 def configure(args):
-	"""Set up log files and associated handlers"""
-	# Configure logging, stderr and file logs
-	logging_level = logging.INFO
-	if args.verbose:
-		logging_level = logging.DEBUG
-
-	logFormatter = logging.Formatter("%(asctime)s - [%(levelname)-4.8s] - %(filename)s %(lineno)d - %(message)s")
-	rootLogger = logging.getLogger()
-	rootLogger.setLevel(logging.DEBUG)
-
-	# Set project-level logging
-	if args.module_name is not None:
-		logfile_basename = f"{dt.today().strftime('%Y-%m-%d_%H-%M-%S')}_{args.module_name}.log"
-	rpath = os.path.realpath(args.path[0])
-	if os.path.isdir(rpath):
-		dname = rpath
-	else:
-		dname = os.path.dirname(rpath)
-	lfp = os.path.join(dname, logfile_basename) # base log file path
-	fileHandler = logging.FileHandler(lfp)
-	fileHandler.setFormatter(logFormatter)
-	fileHandler.setLevel(logging.DEBUG) # always show debug statements in log file
-	rootLogger.addHandler(fileHandler)
-
-	sdfp = os.path.join('/', 'var', 'log', 'rawtools', args.module_name) # system directory file path
-	if not os.path.exists(sdfp):
-		os.makedirs(sdfp)
-	slfp = os.path.join(sdfp, logfile_basename) # system log file path
-	syslogFileHandler = logging.FileHandler(slfp)
-	syslogFileHandler.setFormatter(logFormatter)
-	syslogFileHandler.setLevel(logging.DEBUG) # always show debug statements in log file
-	rootLogger.addHandler(syslogFileHandler)
-
-	consoleHandler = logging.StreamHandler()
-	consoleHandler.setFormatter(logFormatter)
-	consoleHandler.setLevel(logging_level)
-	rootLogger.addHandler(consoleHandler)
-
-	logging.debug(f'Running {args.module_name} {__version__}')
-	logging.debug(f"Command: {args}")
+    """Set up log files and associated handlers"""
+    # Configure logging, stderr and file logs
+    logging_level = logging.INFO
+    if args.verbose:
+        logging_level = logging.DEBUG
+
+    logFormatter = logging.Formatter("%(asctime)s - [%(levelname)-4.8s] - %(filename)s %(lineno)d - %(message)s")
+    rootLogger = logging.getLogger()
+    rootLogger.setLevel(logging.DEBUG)
+
+    # Set project-level logging
+    if args.module_name is not None:
+        logfile_basename = f"{dt.today().strftime('%Y-%m-%d_%H-%M-%S')}_{args.module_name}.log"
+    if args.outdir is not None:
+        rpath = os.path.realpath(args.outdir)
+    else:
+        rpath = os.path.realpath(args.path[0])
+    if os.path.isdir(rpath):
+        dname = rpath
+    else:
+        dname = os.path.dirname(rpath)
+    lfp = os.path.join(dname, logfile_basename) # base log file path
+    fileHandler = logging.FileHandler(lfp)
+    fileHandler.setFormatter(logFormatter)
+    fileHandler.setLevel(logging.DEBUG) # always show debug statements in log file
+    rootLogger.addHandler(fileHandler)
+
+    sdfp = os.path.join('/', 'var', 'log', 'rawtools', args.module_name) # system directory file path
+    if not os.path.exists(sdfp):
+        os.makedirs(sdfp)
+    slfp = os.path.join(sdfp, logfile_basename) # system log file path
+    syslogFileHandler = logging.FileHandler(slfp)
+    syslogFileHandler.setFormatter(logFormatter)
+    syslogFileHandler.setLevel(logging.DEBUG) # always show debug statements in log file
+    rootLogger.addHandler(syslogFileHandler)
+
+    consoleHandler = logging.StreamHandler()
+    consoleHandler.setFormatter(logFormatter)
+    consoleHandler.setLevel(logging_level)
+    rootLogger.addHandler(consoleHandler)
+
+    logging.debug(f'Running {args.module_name} {__version__}')
+    logging.debug(f"Command: {args}")

rawtools/qualitycontrol.py

@@ -215,7 +215,8 @@ def get_top_down_projection(args, fp):
             array_buffer = arr.tobytes()
             pngImage = Image.new("I", arr.T.shape)
             pngImage.frombytes(array_buffer, "raw", "I;16")
-            pngImage.save(ofp)
+            if not args.dryrun:
+                pngImage.save(ofp)
 
         except Exception as err:
             logging.error(err)
@@ -332,8 +333,9 @@ def get_side_projection(args, fp):
             pngImage = Image.new("I", arr.shape)
             logging.debug(f"pngImage.frombytes(array_buffer, 'raw', \"I;16\")")
             pngImage.frombytes(array_buffer, "raw", "I;16")
-            logging.debug(f"pngImage.save(ofp)")
-            pngImage.save(ofp)
+            if not args.dryrun:
+                logging.debug(f"pngImage.save(ofp)")
+                pngImage.save(ofp)
 
             if "step" in args and args.step:
                 try:
@@ -362,7 +364,8 @@ def get_side_projection(args, fp):
                         draw.text((110, text_y), str(slice_index), font=font, fill=fill)
                         # Add line
                         draw.line((0, slice_index, 100, slice_index), fill=fill)
-                    img.save(ofp)
+                    if not args.dryrun:
+                        img.save(ofp)
                 except:
                     raise
 
@@ -453,7 +456,8 @@ def get_slice(args, fp):
         array_buffer = arr.tobytes()
         pngImage = Image.new("I", arr.T.shape)
         pngImage.frombytes(array_buffer, "raw", "I;16")
-        pngImage.save(ofp)
+        if not args.dryrun:
+            pngImage.save(ofp)
     except Exception as err:
         logging.error(err)
         sys.exit(1)
@@ -532,6 +536,8 @@ def main(args):
         for fp in args.path:
             # Set working directory for file
             args.cwd = os.path.dirname(os.path.abspath(fp))
+            if args.outdir is not None:
+                args.cwd = os.path.realpath(args.outdir)
             fp = os.path.abspath(fp)
 
             # Format file size

setup.py

@@ -65,7 +65,7 @@
     setup_requires=setup_requirements,
     test_suite='tests',
     tests_require=test_requirements,
-    url='https://github.com/tparkerd/python-rawtools',
+    url='https://github.com/Topp-Roots-Lab/python-rawtools',
     version='0.3.0',
     zip_safe=False,
 )