Better support for 2D images

- Z resolution is no longer required
- Fixed loading 2D images from LIF files

organoid_tracker/core/images.py

@@ -285,7 +285,12 @@ def resolution(self, allow_incomplete: bool = False) -> ImageResolution:
         the data has multiple time points, but no time resolution has been set.
         """
         require_time_resolution = self.first_time_point_number() != self.last_time_point_number()
-        if not allow_incomplete and self._resolution.is_incomplete(require_time_resolution=require_time_resolution):
+        require_z = False
+        image_size = self._image_loader.get_image_size_zyx()
+        if image_size is not None and image_size[0] > 1:
+            require_z = True  # We have 3D images, require a Z resolution
+        if not allow_incomplete and self._resolution.is_incomplete(require_time_resolution=require_time_resolution,
+                                                                   require_z=require_z):
             raise UserError("No image resolution set", "No image resolution was set. Please set a resolution first."
                                                        " This can be done in the Edit menu of the program.")
         return self._resolution
@@ -328,7 +333,9 @@ def set_timings(self, timings: Optional[ImageTimings]):
         self._timings = timings
 
         # Also keep time resolution in sync
-        self._resolution.time_point_interval_m = timings.get_time_m_since_previous(TimePoint(1))
+        self._resolution = ImageResolution(self._resolution.pixel_size_x_um, self._resolution.pixel_size_y_um,
+                                           self._resolution.pixel_size_z_um,
+                                           timings.get_time_m_since_previous(TimePoint(1)))
 
     def is_inside_image(self, position: Position, *, margin_xy: int = 0, margin_z: int = 0) -> Optional[bool]:
         """Checks if the given position is inside the images. If there are no images loaded, this returns None. Any

organoid_tracker/core/resolution.py

@@ -44,12 +44,15 @@ def __repr__(self) -> str:
         return f"ImageResolution({self.pixel_size_x_um}, {self.pixel_size_y_um}, {self.pixel_size_z_um}," \
                f" {self.time_point_interval_m})"
 
-    def is_incomplete(self, *, require_time_resolution: bool = True) -> bool:
+    def is_incomplete(self, *, require_time_resolution: bool = True, require_z: bool = True) -> bool:
         """Returns True if the x, y, z and/or t resolution is zero. Otherwise it returns False."""
         if require_time_resolution:
             if self.time_point_interval_m == 0 or self.time_point_interval_m == float("inf"):
                 return True
-        return 0 in self.pixel_size_zyx_um
+        if require_z:
+            if self.pixel_size_z_um == 0:
+                return True
+        return self.pixel_size_x_um == 0 or self.pixel_size_y_um == 0
 
 
 # See typehint at beginning of ImageResolution class

organoid_tracker/image_loading/imsfile_image_loader.py

@@ -732,15 +732,15 @@ class _ImsImageLoader(ImageLoader):
     def __init__(self, file_name: str, min_time_point: Optional[int], max_time_point: Optional[int]):
         self._reader = _ImsReader(file_name)
         self._min_time_point = 0 if min_time_point is None else min_time_point
-        self._max_time_point = self._reader.TimePoints if max_time_point is None else max_time_point
+        self._max_time_point = self._reader.TimePoints - 1 if max_time_point is None else max_time_point
 
     def get_3d_image_array(self, time_point: TimePoint, image_channel: ImageChannel) -> Optional[ndarray]:
         time_point_number = time_point.time_point_number()
         if time_point_number < self.first_time_point_number() or time_point_number > self.last_time_point_number():
             return None
         if image_channel.index_zero < 0 or image_channel.index_zero >= self._reader.Channels:
             return None
-        array = self._reader[time_point_number - 1, image_channel.index_zero]
+        array = self._reader[time_point_number, image_channel.index_zero]
         if not numpy.any(array):
             return None  # Got an all-zero array, ignore
         return array
@@ -753,7 +753,7 @@ def get_2d_image_array(self, time_point: TimePoint, image_channel: ImageChannel,
             return None
         if image_z < 0 or image_z >= self._reader.shape[2]:
             return None
-        array = self._reader[time_point_number - 1, image_channel.index_zero, image_z]
+        array = self._reader[time_point_number, image_channel.index_zero, image_z]
         if not numpy.any(array):
             return None  # Got an all-zero array, ignore
         return array
@@ -762,10 +762,10 @@ def get_image_size_zyx(self) -> Optional[Tuple[int, int, int]]:
         return self._reader.shape[-3], self._reader.shape[-2], self._reader.shape[-1]
 
     def first_time_point_number(self) -> int:
-        return max(self._min_time_point, 1)
+        return max(self._min_time_point, 0)
 
     def last_time_point_number(self) -> int:
-        return min(self._max_time_point, self._reader.TimePoints)
+        return min(self._max_time_point, self._reader.TimePoints - 1)
 
     def get_channel_count(self) -> int:
         return self._reader.Channels
@@ -793,7 +793,7 @@ def get_time_resolution_m(self) -> float:
     def get_timings(self) -> Optional[ImageTimings]:
         if "DataSetTimes" in self._reader.hf:
             timespans_s = [float(moment[2] / 1_000_000_000) for moment in self._reader.hf["DataSetTimes"]["Time"]]
-            timespans_s = [0.0] + timespans_s
             timespans_s = numpy.array(timespans_s, dtype=numpy.float64)
-            return ImageTimings(1, timespans_s / 60)
+            timespans_s -= timespans_s[0]
+            return ImageTimings(0, timespans_s / 60)
         return None

organoid_tracker/image_loading/liffile_image_loader.py

@@ -139,6 +139,8 @@ def get_3d_image_array(self, time_point: TimePoint, image_channel: ImageChannel)
             return None
 
         array = self._serie.getFrame(channel=image_channel.index_zero, T=time_point.time_point_number())
+        if len(array.shape) == 2:  # Convert to 3D
+            array = array[numpy.newaxis, :, :]
         if array.dtype != numpy.uint8:  # Saves memory
             array = bits.image_to_8bit(array)
         if self._inverted_z:

organoid_tracker/imaging/list_io.py

@@ -67,3 +67,13 @@ def _contains_images(experiment_json: Dict[str, Any]) -> bool:
         if key.startswith("images_"):
             return True
     return False
+
+
+def count_experiments_in_list_file(open_files_list_file: str) -> int:
+    """Counts the number of experiments in the given file. Used as a quick way to get that number, instead of loading
+    everything."""
+    with open(open_files_list_file, "r", encoding="utf-8") as handle:
+        experiments_json = json.load(handle)
+        if not isinstance(experiments_json, list):
+            raise TypeError("Expected a list in " + open_files_list_file + ", got " + repr(experiments_json))
+        return len(experiments_json)