Partial progress on implementing GUI for batch export

tparkerd · tparkerd · commit 748c4b517cda · 2020-12-17T15:37:26.000-06:00
diff --git a/rawtools/cli.py b/rawtools/cli.py
@@ -4,7 +4,7 @@
 from importlib.metadata import version
 from multiprocessing import cpu_count
 
-from rawtools import convert, generate, nsihdr, qualitycontrol, log, raw2img
+from rawtools import convert, generate, log, nsihdr, qualitycontrol, raw2img
 
 __version__ = version('rawtools')
 
@@ -75,13 +75,20 @@ def raw_nsihdr():
     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('path', metavar='PATH', type=str, nargs='+', help='List of .nsihdr files')
+    parser.add_argument("--gui", action="store_true", default=False, help="Enable GUI")
+    parser.add_argument('path', metavar='PATH', type=str, nargs="+", help='List of .nsihdr files')
     args = parser.parse_args()
 
     args.module_name = 'nsihdr'
     log.configure(args)
 
-    nsihdr.main(args)
+    # Use a GUI to select the source directory
+    if args.gui == True:
+        from rawtools.gui import nsihdr
+        nsihdr.App(args)
+    # Otherwise, assume CLI use
+    else:
+        nsihdr.main(args)
 
 def raw_qc():
     """Quality control tools"""
diff --git a/rawtools/gui/__init__.py b/rawtools/gui/__init__.py
diff --git a/rawtools/gui/nsihdr.py b/rawtools/gui/nsihdr.py
@@ -0,0 +1,94 @@
+""""GUI for NSIHDR conversion tool"""
+
+import logging
+import os
+import tkinter as tk
+from pprint import pformat
+from tkinter import E, N, S, W, filedialog, ttk
+
+from ttkthemes import ThemedTk
+
+class App():
+	def __init__(self, args):
+		self.source = ''
+
+		root = ThemedTk(theme='arc')
+		root.title("Batch Export Tool - NSIHDR to RAW + DAT")
+		root.resizable(False, False)
+		mainframe = ttk.Frame(root, padding="16 16")
+		mainframe.grid(column=0, row=0, sticky=(N, S, E, W))
+		mainframe.columnconfigure(0, weight=1)
+
+		# Source folder selection
+		src_intro_label_text = "Choose a directory that contains NSIHDR."
+		src_intro_label = ttk.Label(mainframe, text=src_intro_label_text)
+		src_intro_label.grid(row=0, column=0, columnspan=3, sticky=(E,W), pady="0 8")
+
+		src_label = ttk.Label(mainframe, text="Source Directory:")
+		src_label.grid(row=1, column=0, sticky=W, pady="0 8")
+
+		self.src = tk.StringVar()
+		self.src.set(self.source)
+		# # Add event handling to changes to the source directory text field
+		self.src.trace("w", lambda value = self.src: self.scan_folder([value]))
+		self.src_entry = ttk.Entry(mainframe, textvariable = self.src, width = 100)
+		self.src_entry.grid(row=2, column=0, sticky=(E, W), padx="0 8", pady="0 16")
+
+		self.src_folder_btn = ttk.Button(mainframe, text = 'Select Folder', command=self.choose_src)
+		self.src_folder_btn.grid(row=2, column=1, pady="0 16", padx="8 0")
+
+		# Export data
+		self.export_btn = ttk.Button(mainframe, text = 'export', command=self.export)
+		self.export_btn.grid(row=12, column=0, pady="0 8", columnspan=3)
+
+
+		# Center window on screen
+		root.update() # virtual pre-render of GUI to calculate actual sizes
+		w = root.winfo_reqwidth()
+		h = root.winfo_reqheight()
+		logging.debug(f"Root width: {w}")
+		logging.debug(f"Root height: {h}")
+		ws = root.winfo_screenwidth()
+		hs = root.winfo_screenheight()
+		# calculate position x, y
+		x = (ws/2) - (w/2)    
+		y = (hs/2) - (h/2)
+		root.geometry('+%d+%d' % (x, y))
+
+
+		# Display window to user
+		root.mainloop()
+
+	def choose_src(self):
+		"""Select a folder to act as data source"""
+		self.source = filedialog.askdirectory(initialdir=self.source, title="Choose directory")
+		logging.debug(f'Selected folder: {self.source}')
+		self.src.set(self.source)
+		# self.files = scan_folder(path = [self.source])
+
+	def scan_folder(path):
+		# Gather all files
+		logging.info(path)
+		files = []
+		for p in path:
+			for root, _, files in os.walk(p):
+				for filename in files:
+					files.append(os.path.join(root, filename))
+					logging.info(filename)
+
+		# Append any loose, explicitly defined paths to .nsihdr files
+		files.extend([ f for f in path if f.endswith('.nsihdr') ])
+
+		# Filter out non-NSIHDR files
+		files = [ f for f in files if f.endswith('.nsihdr') ]
+
+		# Get all RAW files
+		logging.debug(f"All files: {pformat(files)}")
+		files = list(set(files)) # remove duplicates
+		logging.debug(f"Unique files: {pformat(files)}")
+
+		return files
+
+	def export(self):
+		logging.debug("PLACEHOLDER - EXPORT DATA")
+
diff --git a/rawtools/nsihdr.py b/rawtools/nsihdr.py
@@ -6,6 +6,7 @@
 import re
 import sys
 from multiprocessing import Pool, cpu_count
+from pprint import pformat
 from time import time
 
 import numpy as np
@@ -21,102 +22,14 @@
 sys.path.append(includesdir)
 from rawtools import nsiefx
 
-
-def write_metadata(args, metadata):
-	"""Generates a .dat file from information gathered from an .nsihdr file
-
-	NOTE(tparker): Temporarily, I am writing the minimum and maximum values found
-	in the 32-bit float version of the files in case we ever need to convert the
-	uint16 version back to float32.
-
-	Args:
-		args (ArgumentParser): user arguments from `argparse`
-		metadata (dict): dictionary of metadata created from reading .nsihdr file
-	"""
-	ObjectFileName = args.output
-	resolution = ' '.join(metadata['dimensions'])
-	slice_thickness = ' '.join([ str(rr) for rr in metadata['resolution_rounded'] ])
-	dat_filepath = f'{os.path.splitext(args.output)[0]}.dat'
-	output_string = f"""ObjectFileName: {ObjectFileName}\nResolution:     {resolution}\nSliceThickness: {slice_thickness}\nFormat:         {metadata['bit_depth_type']}\nObjectModel:    {metadata['ObjectModel']}"""
-
-	dat.write(dat_filepath, metadata['dimensions'], metadata['resolution_rounded'])
-	# with open(dat_filepath, 'w') as ofp:
-	#   print(f'Generating {dat_filepath}')
-	#   ofp.write(output_string)
-
-	bounds_filepath = os.path.join(args.cwd, f'{os.path.splitext(args.output)[0]}.float32.range')
-	with open(bounds_filepath, 'w') as ofp:
-		print(f'Generating {bounds_filepath}')
-		bounds = f'{INITIAL_LOWER_BOUND} {INITIAL_UPPER_BOUND}'
-		ofp.write(bounds)
-
-def read_nsihdr(args, fp):
-	"""Collects relative metadata from .nsihdr file
-
-	Args:
-		fp (str): Input filepath to an .nsihdr file
-
-	Returns:
-		dict: metadata about NSI project
-	"""
-	global INITIAL_LOWER_BOUND
-	global INITIAL_UPPER_BOUND
-
-	with open(fp, 'r') as ifp:
-		document = ifp.readlines()
-
-		source_to_detector_distance = None
-		source_to_table_distance = None
-		bit_depth = None
-		nsidats = []
-
-		bit_depth_query = re.search(bit_depth_pattern, line)
-		if bit_depth_query:
-			bit_depth = int(bit_depth_query.group('value'))
-
-		dimensions_query = re.search(dimensions_pattern, line)
-		if dimensions_query:
-			dimensions = [ dimensions_query.group('x'), dimensions_query.group('z'), dimensions_query.group('num_slices') ]
-
-		# Check if the .nsihdr already contains the data range
-		# If it exists, we only have to read the .nsidat files once instead of twice
-		data_range_query = re.search(data_range_pattern, line)
-		if data_range_query:
-			INITIAL_LOWER_BOUND = float(data_range_query.group('lower_bound'))
-			INITIAL_UPPER_BOUND = float(data_range_query.group('upper_bound'))
-
-		# Temporarily set pitch as 0.127, as it should not change until we get a
-		# new detector
-		pitch = 0.127
-
-		# TODO(tparker): As far as I am aware, the data will always be of type DENSITY
-		ObjectModel = 'DENSITY'
-
-		resolution = ( pitch / source_to_detector_distance ) * source_to_table_distance
-		resolution_rounded = round(resolution, 4)
-		nsidats.sort() # make sure that the files are in alphanumeric order
-
-		return {
-			"datafiles": nsidats,
-			"source_to_detector_distance": source_to_detector_distance,
-			"source_to_table_distance": source_to_table_distance,
-			"pitch": pitch,
-			"resolution": resolution,
-			"resolution_rounded": [resolution_rounded]*3,
-			"bit_depth": bit_depth,
-			"zoom_factor": round(source_to_detector_distance / source_to_table_distance, 2),
-			"bit_depth_type": dat.bitdepth(bit_depth),
-			"ObjectModel": ObjectModel,
-			"dimensions": dimensions
-		}
-
-def process(args, fp, ofp):
+def process(args, fp, export_path):
 	"""Converts NSIHDR files to a single .RAW + .DAT
 
 	Args:
+
 		args (ArgumentParser): user arguments from `argparse`
 		fp (str): filepath to input .NSIHDR file
-		ofp (str): filepath to output .RAW file
+		export_path (str): filepath to output .RAW file
 	"""
 	logging.debug(f'{fp=}')
 
@@ -137,12 +50,10 @@ def process(args, fp, ofp):
 
 		dname = os.path.dirname(fp)
 		bname = os.path.basename(os.path.splitext(fp)[0])
-		export_path = os.path.join(dname, f'{bname}.raw')
-		logging.debug(f"{export_path=}")
 		dat_path = os.path.join(dname, f'{bname}.dat')
-		logging.debug(f"{dat_path=}")
 
 		dat.write(dat_path, dimensions = (width, height, depth), thickness = voxel_size)
+		logging.debug(f"Generated '{dat_path}'")
 
 		if os.path.exists(export_path) and args.force == True:
 			os.remove(export_path)
@@ -152,14 +63,18 @@ def process(args, fp, ofp):
 			logging.warning(f"Removed old '{dat_path}'")
 
 		with open(export_path, 'ab') as raw_ofp:
-			pbar = tqdm(total= depth, desc=f"Exporting {bname}")
+			if not args.verbose:
+				pbar = tqdm(total= depth, desc=f"Exporting {bname}")
 			for n in range(depth):
 				cross_section = v.read_slice(n)
 				cross_section = np.array(cross_section, dtype="float32")
 				cross_section = scale(cross_section, data_min, data_max, 0, 65535).astype(np.uint16)
 				cross_section.tofile(raw_ofp)
-				pbar.update()
-			pbar.close()
+
+				if not args.verbose:
+					pbar.update()
+			if not args.verbose:
+				pbar.close()
 
 def main(args):
 	start_time = time()
@@ -168,48 +83,89 @@ def main(args):
 		# Gather all files
 		args.files = []
 		for p in args.path:
-			for root, dirs, files in os.walk(p):
+			for root, _, files in os.walk(p):
 				for filename in files:
 					args.files.append(os.path.join(root, filename))
 
-		# Append any loose, explicitly defined paths to .RAW files
+		# Append any loose, explicitly defined paths to .nsihdr files
 		args.files.extend([ f for f in args.path if f.endswith('.nsihdr') ])
 
 		# Filter out non-NSIHDR files
 		args.files = [ f for f in args.files if f.endswith('.nsihdr') ]
 
 		# Get all RAW files
-		logging.debug(f"All files: {args.files}")
+		logging.debug(f"All files: {pformat(args.files)}")
 		args.files = list(set(args.files)) # remove duplicates
-		logging.info(f"Found {len(args.files)} volume(s).")
-		logging.debug(f"Unique files: {args.files}")
+		logging.debug(f"Unique files: {pformat(args.files)}")
+
+		# If file overwriting is disabled
+		if not args.force:
+			kept_volumes = []
+			skipped_volumes = []
+			for fp in args.files:
+				dname = os.path.dirname(fp)
+				bname = os.path.basename(os.path.splitext(fp)[0])
+				export_path = os.path.join(dname, f'{bname}.raw')
+				if os.path.exists(export_path) and os.path.isfile(export_path):
+					skipped_volumes.append(export_path)
+				else:
+					kept_volumes.append(export_path)
+			args.files = kept_volumes
+			total_volumes = len(kept_volumes) + len(skipped_volumes)
+			logging.debug(f"{kept_volumes=}")
+			logging.debug(f"{skipped_volumes=}")
+
+			logging.info(f"Found {total_volumes} volume(s). (Unchanged: {len(kept_volumes)}, Skipped: {len(skipped_volumes)})")
+
+		# Otherwise, overwrite files
+		else:
+			unprocessed_volumes = []
+			existing_volumes = []
+			for fp in args.files:
+				dname = os.path.dirname(fp)
+				bname = os.path.basename(os.path.splitext(fp)[0])
+				export_path = os.path.join(dname, f'{bname}.raw')
+				if os.path.exists(export_path) and os.path.isfile(export_path):
+					existing_volumes.append(export_path)
+				else:
+					unprocessed_volumes.append(export_path)
+			total_volumes = len(existing_volumes) + len(unprocessed_volumes)
+
+			logging.debug(f"{existing_volumes=}")
+			logging.debug(f"{unprocessed_volumes=}")
+
+			logging.info(f"Found {total_volumes} volume(s). (Overwriting: {len(existing_volumes)}, New: {len(unprocessed_volumes)})")
+
 	except Exception as err:
 		logging.error(err)
 		raise err
 	else:
 		# For each provided volume...
-		pbar = tqdm(total = len(args.files), desc=f"Overall progress")
+		if not args.verbose:
+			pbar = tqdm(total = len(args.files), desc=f"Overall progress")
 		for fp in args.files:
 			logging.debug(f"Processing '{fp}'")
-			ofp_directory = os.path.dirname(fp)
-			logging.debug(f"{ofp_directory=}")
-			ofp_filename = os.path.basename(os.path.splitext(fp)[0])
-			logging.debug(f"{ofp_filename=}")
-			ofp = os.path.join(ofp_directory, ofp_filename)
-			logging.debug(f"{ofp=}")
+			dname = os.path.dirname(fp)
+			bname = os.path.basename(os.path.splitext(fp)[0])
+			export_path = os.path.join(dname, f'{bname}.raw')
+			logging.debug(f"{export_path=}")
+			dat_path = os.path.join(dname, f'{bname}.dat')
+			logging.debug(f"{dat_path=}")
 
 			# Determine output location and check for conflicts
-			if os.path.exists(ofp) and os.path.isfile(ofp):
+			if os.path.exists(export_path) and os.path.isfile(export_path):
 				# If file creation not forced, do not process volume, return
 				if args.force == False:
-					logging.info(f"File already exists. Skipping {ofp}.")
+					logging.info(f"File already exists. Skipping {export_path}.")
 					continue
 				# Otherwise, user forced file generation
 				else:
-					logging.warning(f"FileExistsWarning - {ofp}. File will be overwritten.")
+					logging.warning(f"FileExistsWarning - {export_path}. File will be overwritten.")
 
 			# Extract slices and cast to desired datatype
-			process(args, fp, ofp)
+			process(args, fp, export_path)
 
-			pbar.update()
-		pbar.close()
+			if not args.verbose:
+				pbar.update()
+		if not args.verbose:
+			pbar.close()
diff --git a/setup.py b/setup.py
@@ -13,7 +13,7 @@
 with open('HISTORY.rst') as history_file:
     history = history_file.read()
 
-requirements = ['numpy==1.19.3', 'tqdm', 'Pillow', ]
+requirements = ['numpy==1.19.3', 'tqdm', 'Pillow', 'ttkthemes' ]
 
 setup_requirements = ['pytest-runner', ]
 
