Registered image selector fixes

magmap/gui/visualizer.py

@@ -261,7 +261,6 @@ class Visualization(HasTraits):
  # File selection
 
  _filename = File # file browser
- _ignore_filename = False # ignore file update trigger
  _channel_names = Instance(TraitsList)
  _channel = List # selected channels, 0-based
 
@@ -792,10 +791,11 @@ def __init__(self):
  self._drawn_offset = self._curr_offset()
 
  # setup interface for image
+ self._ignore_filename = False # ignore file update trigger
+ self._reset_filename = True # reset when updating loaded image
  if config.filename:
  # show image filename in file selector without triggering update
- self._ignore_filename = True
- self._filename = config.filename
+ self.update_filename(config.filename, True, False)
 
  # create figs after applying Matplotlib style and theme
  rc_params = None
@@ -829,6 +829,10 @@ def __init__(self):
  self._imgadj_max_ignore_update = False
 
  # set up rest of registered images during image setup
+
+ # dictionary of registered image suffix without ext to suffix with
+ # ext of a matching existing file
+ self._reg_img_names: OrderedDict[str, str] = OrderedDict()
  self._main_img_names_avail = TraitsList()
  self._main_img_names = TraitsList()
  self._labels_img_names = TraitsList()
@@ -1541,23 +1545,25 @@ def _setup_for_image(self):
  else [config.roi_size])
 
  # find matching registered images to populate dropdowns
- main_img_names_avail = []
+ self._reg_img_names = OrderedDict()
  for reg_name in config.RegNames:
  # check for potential registered image files
  reg_path = sitk_io.read_sitk(sitk_io.reg_out_path(
  config.filename, reg_name.value), dryrun=True)[1]
  if reg_path:
- # add to list of available suffixes
- main_img_names_avail.append(
- f"{os.path.splitext(reg_name.value)[0]}"
- f"{os.path.splitext(reg_path)[1]}")
- self._labels_img_names.selections = list(main_img_names_avail)
+ # add to list of available suffixes, storing the found
+ # extension to load directly and save to same ext
+ name = libmag.get_filename_without_ext(reg_name.value)
+ self._reg_img_names[name] = (
+ f"{name}{libmag.splitext(reg_path)[1]}")
+ self._labels_img_names.selections = list(self._reg_img_names.keys())
  self._labels_img_names.selections.insert(0, "")
 
  # set any registered names based on loaded images, defaulting to
  # image5d and no labels
  main_suffixes = [self._MAIN_IMG_NAME_DEFAULT]
  labels_suffix = self._labels_img_names.selections[0]
+ main_img_names_avail = list(self._reg_img_names.keys())
  if config.reg_suffixes:
  # use registered suffixes without ext, using first suffix
  # of each type
@@ -1566,15 +1572,17 @@ def _setup_for_image(self):
  if not libmag.is_seq(suffixes):
  suffixes = [suffixes]
  for suffix in suffixes:
- if suffix in main_img_names_avail:
+ suffix_stem = libmag.get_filename_without_ext(suffix)
+ if suffix_stem in main_img_names_avail:
  # move from available to selected suffixes lists
- main_suffixes.append(suffix)
- main_img_names_avail.remove(suffix)
+ main_suffixes.append(suffix_stem)
+ main_img_names_avail.remove(suffix_stem)
  suffix = config.reg_suffixes[config.RegSuffixes.ANNOTATION]
  if suffix:
- suffix = libmag.get_if_within(suffix, 0, "")
- if suffix in self._labels_img_names.selections:
- labels_suffix = suffix
+ suffix_stem = libmag.get_filename_without_ext(
+ libmag.get_if_within(suffix, 0, ""))
+ if suffix_stem in self._labels_img_names.selections:
+ labels_suffix = suffix_stem
 
  # show main image lists in two dropdowns, where selecting a suffix
  # from one list immediately moves it to the other 
@@ -1610,15 +1618,26 @@ def _setup_for_image(self):
  self._rois_selections.selections = list(self._rois_dict.keys())
  self.rois_check_list = _ROI_DEFAULT
 
- def update_filename(self, filename):
+ def update_filename(
+ self, filename: str, ignore: bool = False, reset: bool = True):
  """Update main image filename, triggering image load.
 
  Args:
- filename (str): Path to image file to load.
+ filename: Path to image file to load.
+ ignore: Set to :attr:`_ignore_filename` flag; deafults to False.
+ True to av
+ reset: Set the :attr:`_reset_filename` flag; defaults to False.
+ True to reset additional image parameters such as registered
+ image suffixes.
 
  """
- # reset path so that new path triggers an image load
+ # if old and new filename are the same, no update will be triggered,
+ # so need to set to non-image first
  self._filename = ""
+
+ # update filename, triggering Trait change
+ self._reset_filename = reset
+ self._ignore_filename = ignore
  self._filename = filename
 
  def open_image(self, filename, new_window=True):
@@ -1653,10 +1672,17 @@ def _image_path_updated(self):
  will not be loaded for now.
  """
  if self._ignore_filename or not self._filename:
- # ignore if only updating widget value, without triggering load
+ # avoid triggering file load, eg if only updating widget value;
+ # reset flags
  self._ignore_filename = False
+ self._reset_filename = True
  return
-
+
+ if self._reset_filename:
+ # reset registered suffixes
+ config.reg_suffixes = dict.fromkeys(config.RegSuffixes, None)
+ self._reset_filename = True
+
  # load image if possible without allowing import, deconstructing
  # filename from the selected imported image
  filename, offset, size, reg_suffixes = importer.deconstruct_img_name(
@@ -1694,21 +1720,22 @@ def _reload_images(self):
  if len(atlas_suffixes) == 1:
  # reduce to str if only one element
  atlas_suffixes = atlas_suffixes[0]
- reg_suffixes[config.RegSuffixes.ATLAS] = atlas_suffixes
+ reg_suffixes[config.RegSuffixes.ATLAS] = self._reg_img_names.get(
+ atlas_suffixes)
 
  if self._labels_img_names.selections.index(self._labels_img_name) != 0:
  # add if not the empty first selection
- reg_suffixes[config.RegSuffixes.ANNOTATION] = self._labels_img_name
+ reg_suffixes[
+ config.RegSuffixes.ANNOTATION] = self._reg_img_names.get(
+ self._labels_img_name)
  config.reg_suffixes.update(reg_suffixes)
 
  if self._labels_ref_path:
  # set up labels
  cli.setup_labels([self._labels_ref_path])
 
  # re-setup image
- filename = self._filename
- self._filename = ""
- self._filename = filename
+ self.update_filename(self._filename, reset=False)
 
  @on_trait_change("_channel")
  def update_channel(self):

magmap/io/importer.py

@@ -349,7 +349,7 @@ def deconstruct_img_name(np_filename, sep="_", keep_subimg=False):
  suffix = suffix.value
  suffix_noext = libmag.get_filename_without_ext(suffix)
  suffixi = np_filename.rfind(suffix_noext)
- if suffixi != -1 and os.path.splitext(np_filename)[0].endswith(
+ if suffixi != -1 and libmag.splitext(np_filename)[0].endswith(
  suffix_noext):
  # strip suffix and any ending separator to get base path
  filename = np_filename[:suffixi]

magmap/io/libmag.py

@@ -240,9 +240,8 @@ def match_ext(path, path_to_match):
  return path_to_match
 
 
-def get_filename_without_ext(path):
- """Get filename without extension with support for extensions with
- multiple periods through :meth:`splitext`.
+def get_filename_without_ext(path: str) -> str:
+ """Wrapper to :meth:`splitext` for getting only the filename.
 
  Args:
  path: Full path.
@@ -252,7 +251,7 @@ def get_filename_without_ext(path):
  no extension exists.
  """
  name = os.path.basename(path)
- name_split = os.path.splitext(name)
+ name_split = splitext(name)
  if len(name_split) > 1: return name_split[0]
  return name