Update libCZI and fix shape error

_aicspylibczi/Image.h

@@ -60,7 +60,8 @@ class Image : public SubblockSortable
     , m_shape(std::move(shape_))
     , m_pixelType(pixel_type_)
     , m_xywh(box_)
-  {}
+  {
+  }
 
   size_t calculateIdx(const std::vector<size_t>& indexes_);
 
@@ -144,8 +145,9 @@ class ImageVector : public std::vector<std::shared_ptr<Image>>
     size_t hByWsize = heightByWidth.size();
     charSizes.emplace_back('Y', heightByWidth[0]); // H: 0
     charSizes.emplace_back('X', heightByWidth[1]); // W: 1
-    if (hByWsize > 2)
+    if (hByWsize > 2) {
       charSizes.emplace_back('A', heightByWidth[2]); // A: 3
+    }
     // sort them into decending DimensionIndex Order
     std::sort(charSizes.begin(), charSizes.end(), [&](std::pair<char, size_t> a_, std::pair<char, size_t> b_) {
       return libCZI::Utils::CharToDimension(a_.first) > libCZI::Utils::CharToDimension(b_.first);

_aicspylibczi/Reader.cpp

@@ -185,18 +185,21 @@ Reader::sceneShape(int scene_index_)
         definedDims[dimensionIndexToDimIndex(di_)].emplace(val_);
         return true;
       });
-      if (isMosaic())
+      if (isMosaic()) {
         definedDims[DimIndex::M].emplace(x.first.mIndex());
+      }
     }
-    for (auto x : definedDims)
+    for (auto x : definedDims) {
       tbl.emplace(x.first, std::make_pair(*x.second.begin(), *x.second.rbegin() + 1));
+    }
 
     auto xySize = getSceneYXSize(scene_index_);
     tbl.emplace(DimIndex::Y, std::make_pair(0, xySize.h));
     tbl.emplace(DimIndex::X, std::make_pair(0, xySize.w));
   }
-  if (ImageFactory::numberOfSamples(m_pixelType) > 1)
+  if (ImageFactory::numberOfSamples(m_pixelType) > 1) {
     tbl.emplace(charToDimIndex('A'), std::make_pair(0, ImageFactory::numberOfSamples(m_pixelType)));
+  }
 
   return tbl;
 }
@@ -206,18 +209,11 @@ Reader::getAllSceneYXSize(int scene_index_, bool get_all_matches_)
 {
   std::vector<libCZI::IntRect> result;
   bool hasScene = m_statistics.dimBounds.IsValid(libCZI::DimensionIndex::S);
-  if (!isMosaic() && hasScene) {
-    int sStart(0), sSize(0);
-    m_statistics.dimBounds.TryGetInterval(libCZI::DimensionIndex::S, &sStart, &sSize);
-    if (scene_index_ >= sStart && (sStart + sSize - 1) >= scene_index_ && !m_statistics.sceneBoundingBoxes.empty()) {
-      result.emplace_back(m_statistics.sceneBoundingBoxes[scene_index_].boundingBoxLayer0);
-      return result;
-    }
-  }
 
   libCZI::CDimCoordinate scene_coord; // default constructor
-  if (hasScene && scene_index_ >= 0)
+  if (hasScene && scene_index_ >= 0) {
     scene_coord = libCZI::CDimCoordinate({ { libCZI::DimensionIndex::S, scene_index_ } });
+  }
   SubblockSortable subblocksToFind(&scene_coord, -1, false);
   SubblockIndexVec matches = getMatches(subblocksToFind);
 

_aicspylibczi/Reader.h

@@ -248,7 +248,7 @@ class Reader
   ImagesContainerBase::ImagesContainerBasePtr readMosaic(libCZI::CDimCoordinate plane_coord_,
                                                          float scale_factor_ = 1.0,
                                                          libCZI::IntRect im_box_ = { 0, 0, -1, -1 },
-							 libCZI::RgbFloatColor backGroundColor_ = { 0.0, 0.0, 0.0 });
+                                                         libCZI::RgbFloatColor backGroundColor_ = { 0.0, 0.0, 0.0 });
 
   /*!
    * Convert the libCZI::DimensionIndex to a character
@@ -261,7 +261,6 @@ class Reader
 
   virtual ~Reader() { m_czireader->Close(); }
 
-
   /*!
    * @brief get the shape of the loaded images
    * @param images_ the ImageVector of images to get the shape of
@@ -347,15 +346,15 @@ class Reader
   void checkSceneShapes();
 
   /*!
-  * @brief get the pyramid 0 (acquired data) shape
-  * @param scene_index_ specifies scene but defaults to the first scene,
-  * Scenes can have different sizes
-  * @return std::vector<libCZI::IntRect> containing (x0, y0, w, h)
-  */
+   * @brief get the pyramid 0 (acquired data) shape
+   * @param scene_index_ specifies scene but defaults to the first scene,
+   * Scenes can have different sizes
+   * @return std::vector<libCZI::IntRect> containing (x0, y0, w, h)
+   */
   libCZI::IntRect getSceneYXSize(int scene_index_ = -1)
   {
     std::vector<libCZI::IntRect> matches = getAllSceneYXSize(scene_index_);
-    return matches.empty() ? libCZI::IntRect{ 0,0,0,0 } : matches.front();
+    return matches.empty() ? libCZI::IntRect{ 0, 0, 0, 0 } : matches.front();
   }
 
   /*!
@@ -368,7 +367,6 @@ class Reader
   std::vector<libCZI::IntRect> getAllSceneYXSize(int scene_index_ = -1, bool get_all_matches_ = false);
 
   libCZI::PixelType getFirstPixelType();
-
 };
 
 }

aicspylibczi/CziFile.py

@@ -552,7 +552,13 @@ def read_image(self, **kwargs):
         image, shape = self.reader.read_selected(plane_constraints, m_index, cores)
         return image, shape
 
-    def read_mosaic(self, region: Tuple = None, scale_factor: float = 1.0, background_color: Tuple = None, **kwargs):
+    def read_mosaic(
+        self,
+        region: Tuple = None,
+        scale_factor: float = 1.0,
+        background_color: Tuple = None,
+        **kwargs,
+    ):
         """
         Reads a mosaic file and returns an image corresponding to the specified dimensions. If the file is more than
         a 2D sheet of pixels, meaning only one channel, z-slice, time-index, etc then the kwargs must specify the
@@ -619,7 +625,9 @@ def read_mosaic(self, region: Tuple = None, scale_factor: float = 1.0, backgroun
             tmp.b = background_color[2]
             background_color = tmp
 
-        img = self.reader.read_mosaic(plane_constraints, scale_factor, region, background_color)
+        img = self.reader.read_mosaic(
+            plane_constraints, scale_factor, region, background_color
+        )
 
         return img