Merge pull request #41 from OmooLab/feature/dev

Feature/dev

.gitignore

@@ -133,4 +133,6 @@ blendcache_*
 
 .secrets
 
+.vdb
+
 !scipy_ndimage/*/**

bioxelnodes/__init__.py

@@ -1,5 +1,6 @@
 import bpy
 
+from .props import BIOXELNODES_LayerListUL
 from . import auto_load
 from . import menus
 
@@ -9,11 +10,17 @@
 
 def register():
     auto_load.register()
-    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
+    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty(
+        default=1.0)
     bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
+    bpy.types.WindowManager.bioxelnodes_layer_list_UL = bpy.props.PointerProperty(
+        type=BIOXELNODES_LayerListUL)
     menus.add()
 
 
 def unregister():
     menus.remove()
+    del bpy.types.WindowManager.bioxelnodes_progress_factor
+    del bpy.types.WindowManager.bioxelnodes_progress_text
+    del bpy.types.WindowManager.bioxelnodes_layer_list_UL
     auto_load.unregister()

bioxelnodes/bioxel/layer.py

@@ -2,12 +2,10 @@
 import numpy as np
 
 from . import scipy
-from . import skimage as ski
 from . import scipy as ndi
 
 # 3rd-party
 import transforms3d
-
 # TODO: turn to dataclasses
 
 
@@ -71,23 +69,27 @@ def max(self):
     def copy(self):
         return copy.deepcopy(self)
 
-    def fill(self, value: float, mask: np.ndarray):
+    def fill(self, value: float, mask: np.ndarray, smooth: int = 0):
         mask_frames = ()
         if mask.ndim == 4:
             if mask.shape[0] != self.frame_count:
                 raise Exception("Mask frame count is not same as ")
             for f in range(self.frame_count):
                 mask_frame = mask[f, :, :, :]
-                mask_frame = scipy.minimum_filter(
-                    mask_frame.astype(np.float32), size=3)
+                if smooth > 0:
+                    mask_frame = scipy.minimum_filter(mask_frame.astype(np.float32),
+                                                      mode="nearest",
+                                                      size=smooth)
                 # mask_frame = scipy.median_filter(
                 #     mask_frame.astype(np.float32), size=2)
                 mask_frames += (mask_frame,)
         elif mask.ndim == 3:
             for f in range(self.frame_count):
                 mask_frame = mask[:, :, :]
-                mask_frame = scipy.minimum_filter(
-                    mask_frame.astype(np.float32), size=3)
+                if smooth > 0:
+                    mask_frame = scipy.minimum_filter(mask_frame.astype(np.float32),
+                                                      mode="nearest",
+                                                      size=smooth)
                 # mask_frame = scipy.median_filter(
                 #     mask_frame.astype(np.float32), size=2)
                 mask_frames += (mask_frame,)
@@ -98,20 +100,19 @@ def fill(self, value: float, mask: np.ndarray):
         _mask = np.expand_dims(_mask, axis=-1)
         self.data = _mask * value + (1-_mask) * self.data
 
-    def resize(self, shape: tuple, progress_callback=None):
+    def resize(self, shape: tuple, smooth: int = 0, progress_callback=None):
         if len(shape) != 3:
             raise Exception("Shape must be 3 dim")
 
         data = self.data
-        order = 0 if self.dtype == bool else 1
 
-        # TXYZC > TXYZ
-        if self.kind in ['label', 'scalar']:
-            data = np.amax(data, -1)
+        # # TXYZC > TXYZ
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.amax(data, -1)
 
         # if self.kind in ['scalar']:
         #     dtype = data.dtype
-            # data = data.astype(np.float32)
+        # data = data.astype(np.float32)
 
         data_frames = ()
         for f in range(self.frame_count):
@@ -122,13 +123,22 @@ def resize(self, shape: tuple, progress_callback=None):
             #                    shape,
             #                    preserve_range=True,
             #                    anti_aliasing=data.dtype.kind != "b")
+            frame = data[f, :, :, :, :]
+            if smooth > 0:
+                frame = scipy.median_filter(frame.astype(np.float32),
+                                            mode="nearest",
+                                            size=smooth)
 
             factors = np.divide(self.shape, shape)
             zoom_factors = [1 / f for f in factors]
-            frame = ndi.zoom(data[f, :, :, :],
-                             zoom_factors,
+            order = 0 if frame.dtype == bool else 1
+            frame = ndi.zoom(frame,
+                             zoom_factors+[1.0],
+                             mode="nearest",
+                             grid_mode=False,
                              order=order)
-
+            if smooth > 0:
+                frame = frame.astype(self.dtype)
             data_frames += (frame,)
 
         data = np.stack(data_frames)
@@ -137,7 +147,10 @@ def resize(self, shape: tuple, progress_callback=None):
         #     data = data.astype(dtype)
 
         # TXYZ > TXYZC
-        if self.kind in ['label', 'scalar']:
-            data = np.expand_dims(data, axis=-1)  # expend channel
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.expand_dims(data, axis=-1)  # expend channel
 
         self.data = data
+
+        mat_scale = transforms3d.zooms.zfdir2aff(factors[0])
+        self.affine = np.dot(self.affine, mat_scale)

bioxelnodes/bioxel/parse.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 import numpy as np
-from .layer import Layer
 
 # 3rd-party
 import SimpleITK as sitk
@@ -42,7 +41,8 @@
 SEQUENCE_EXTS = ['.bmp', '.BMP',
                  '.jpg', '.JPG', '.jpeg', '.JPEG',
                  '.tif', '.TIF', '.tiff', '.TIFF',
-                 '.png', '.PNG']
+                 '.png', '.PNG',
+                 '.mrc']
 
 
 def get_ext(filepath: Path) -> str:
@@ -64,18 +64,40 @@ def get_ext(filepath: Path) -> str:
         return filepath.suffix
 
 
-def get_file_name(filepath: Path):
+def get_filename(filepath: Path):
     ext = get_ext(filepath)
-    return filepath.name.removesuffix(ext).replace(" ", "-")
+    return filepath.name.removesuffix(ext)
 
 
-def get_file_number(filepath: Path) -> str:
-    name = get_file_name(filepath)
+def get_filename_parts(filepath: Path) -> str:
+    def has_digits(s):
+        return any(char.isdigit() for char in s)
+
+    name = get_filename(filepath)
+    parts = name.replace(".", " ").replace("_", " ").split(" ")
+    skip_prefixs = ["CH", "ch", "channel"]
+    number_part = None
+    number_part_i = None
+
+    for i, part in enumerate(parts[::-1]):
+        if has_digits(part):
+            if not any([part.startswith(prefix) for prefix in skip_prefixs]):
+                number_part = part
+                number_part_i = len(parts)-i
+                break
+
+    if number_part is None:
+        return name, "", ""
+
+    prefix_parts = parts[:number_part_i-1]
+    prefix_parts_count = sum([len(part)+1 for part in prefix_parts])
+
     digits = ""
+    suffix = ""
 
     # Iterate through the characters in reverse order
     started = False
-    for char in name[::-1]:
+    for char in number_part[::-1]:
         if char.isdigit():
             started = True
             # If the character is a digit, add it to the digits string
@@ -84,29 +106,42 @@ def get_file_number(filepath: Path) -> str:
             if started:
                 # If a non-digit character is encountered, stop the loop
                 break
+            else:
+                suffix += char
+
+    digits = digits[::-1]
+
+    prefix_parts_count += len(number_part) - \
+        len(digits) - len(suffix)
 
     # Reverse the digits string to get the correct order
-    return digits[::-1]
+    prefix = name[:prefix_parts_count]
+    suffix = name[prefix_parts_count+len(digits):]
 
+    return prefix, digits, suffix
 
-def get_sequence_name(filepath: Path) -> str:
-    name = get_file_name(filepath)
-    number = get_file_number(filepath)
-    return name.removesuffix(number)
 
+def get_file_no_digits_name(filepath: Path) -> str:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    prefix = remove_end_str(prefix, "_")
+    prefix = remove_end_str(prefix, ".")
+    prefix = remove_end_str(prefix, "-")
+    prefix = remove_end_str(prefix, " ")
+    return prefix + suffix
 
-def get_sequence_index(filepath: Path) -> int:
-    number = get_file_number(filepath)
-    return int(number) if number != "" else 0
+
+def get_file_index(filepath: Path) -> int:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    return int(digits) if digits != "" else 0
 
 
 def collect_sequence(filepath: Path):
     file_dict = {}
     for f in filepath.parent.iterdir():
         if f.is_file() \
                 and get_ext(filepath) == get_ext(f) \
-                and get_sequence_name(filepath) == get_sequence_name(f):
-            index = get_sequence_index(f)
+                and get_file_no_digits_name(filepath) == get_file_no_digits_name(f):
+            index = get_file_index(f)
             file_dict[index] = f
 
     # reomve isolated seq file
@@ -124,7 +159,13 @@ def collect_sequence(filepath: Path):
     return sequence
 
 
-def parse_volumetric_data(data_file: str, series_id="", progress_callback=None) -> Layer:
+def remove_end_str(string: str, end: str):
+    while string.endswith(end) and len(string) > 0:
+        string = string.removesuffix(end)
+    return string
+
+
+def parse_volumetric_data(data_file: str, series_id="", progress_callback=None):
     """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
 
     Args:
@@ -139,7 +180,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
     ext = get_ext(data_path)
 
     if progress_callback:
-        progress_callback(0, "Reading the Data...")
+        progress_callback(0.0, "Reading the Data...")
 
     is_sequence = False
     if ext in SEQUENCE_EXTS:
@@ -181,7 +222,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             elif mrc.is_volume_stack():
                 data = np.expand_dims(data, axis=-1)  # expend channel
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
             spacing = (mrc.voxel_size.x,
                        mrc.voxel_size.y,
                        mrc.voxel_size.z)
@@ -245,7 +286,7 @@ def parse_volumetric_data(data_file: str, series_id="", progress_callback=None)
             except:
                 ...
 
-            name = get_file_name(data_path)
+            name = get_file_no_digits_name(data_path)
         except:
             ...
 
@@ -297,10 +338,10 @@ def get_meta(key):
 
         elif ext in SEQUENCE_EXTS and is_sequence:
             itk_image = sitk.ReadImage(sequence)
-            name = get_sequence_name(data_path)
+            name = get_file_no_digits_name(data_path)
         else:
             itk_image = sitk.ReadImage(data_path)
-            name = get_file_name(data_path)
+            name = get_filename(data_path)
 
         # for key in itk_image.GetMetaDataKeys():
         #     print(f"{key},{itk_image.GetMetaData(key)}")