deepliif 1.1.10__tar.gz → 1.1.11__tar.gz

{deepliif-1.1.10/deepliif.egg-info → deepliif-1.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.10
+Version: 1.1.11
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -24,6 +24,8 @@ License-File: LICENSE.md
     |
     <a href="https://onlinelibrary.wiley.com/share/author/4AEBAGEHSZE9GDP3H8MN?target=10.1111/his.15048">Histopathology'23</a>
     |
+    <a href="https://arxiv.org/abs/2405.08169">MICCAI'24</a>
+    |
     <a href="https://deepliif.org/">Cloud Deployment</a>
     |
     <a href="https://nadeemlab.github.io/DeepLIIF/">Documentation</a>
@@ -250,7 +252,7 @@ The plugin also supports submitting multiple ROIs at once:
 ## Cloud Deployment
 If you don't have access to GPU or appropriate hardware and don't want to install ImageJ, we have also created a [cloud-native DeepLIIF deployment](https://deepliif.org) with a user-friendly interface to upload images, visualize, interact, and download the final results.
 
-![DeepLIIF Website Demo](images/deepliif-website-demo-03.gif)
+![DeepLIIF Website Demo](images/deepliif-website-demo-04.gif)
 
 ## Cloud API Endpoints
 
@@ -549,4 +551,11 @@ If you find our work useful in your research or if you use parts of this code or
   year = {2023},
   doi = {https://doi.org/10.1111/his.15048}
 }
+
+@article{zehra2024deepliifstitch,
+author = {Zehra, Talat and Marino, Joseph and Wang, Wendy and Frantsuzov, Grigoriy and Nadeem, Saad},
+title = {Rethinking Histology Slide Digitization Workflows for Low-Resource Settings},
+journal = {International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
+year = {2024}
+}
 ```

{deepliif-1.1.10 → deepliif-1.1.11}/README.md

@@ -13,6 +13,8 @@
     |
     <a href="https://onlinelibrary.wiley.com/share/author/4AEBAGEHSZE9GDP3H8MN?target=10.1111/his.15048">Histopathology'23</a>
     |
+    <a href="https://arxiv.org/abs/2405.08169">MICCAI'24</a>
+    |
     <a href="https://deepliif.org/">Cloud Deployment</a>
     |
     <a href="https://nadeemlab.github.io/DeepLIIF/">Documentation</a>
@@ -239,7 +241,7 @@ The plugin also supports submitting multiple ROIs at once:
 ## Cloud Deployment
 If you don't have access to GPU or appropriate hardware and don't want to install ImageJ, we have also created a [cloud-native DeepLIIF deployment](https://deepliif.org) with a user-friendly interface to upload images, visualize, interact, and download the final results.
 
-![DeepLIIF Website Demo](images/deepliif-website-demo-03.gif)
+![DeepLIIF Website Demo](images/deepliif-website-demo-04.gif)
 
 ## Cloud API Endpoints
 
@@ -538,4 +540,11 @@ If you find our work useful in your research or if you use parts of this code or
   year = {2023},
   doi = {https://doi.org/10.1111/his.15048}
 }
+
+@article{zehra2024deepliifstitch,
+author = {Zehra, Talat and Marino, Joseph and Wang, Wendy and Frantsuzov, Grigoriy and Nadeem, Saad},
+title = {Rethinking Histology Slide Digitization Workflows for Low-Resource Settings},
+journal = {International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
+year = {2024}
+}
 ```

{deepliif-1.1.10 → deepliif-1.1.11}/deepliif/models/__init__.py

@@ -293,10 +293,11 @@ def is_empty_old(tile):
 
 
 def is_empty(tile):
+    thresh = 15
     if isinstance(tile, list): # for pair of tiles, only mark it as empty / no need for prediction if ALL tiles are empty
-        return all([True if np.max(image_variance_rgb(tile)) < 15 else False for t in tile])
+        return all([True if np.max(image_variance_rgb(t)) < thresh else False for t in tile])
     else:
-        return True if np.max(image_variance_rgb(tile)) < 15 else False
+        return True if np.max(image_variance_rgb(tile)) < thresh else False
 
 
 def run_wrapper(tile, run_fn, model_path, eager_mode=False, opt=None):
@@ -368,8 +369,8 @@ def inference_old(img, tile_size, overlap_size, model_path, use_torchserve=False
     return images
 
 
-def inference(img, tile_size, overlap_size, model_path, use_torchserve=False, eager_mode=False,
-              color_dapi=False, color_marker=False, opt=None):
+def inference_old2(img, tile_size, overlap_size, model_path, use_torchserve=False, eager_mode=False,
+                   color_dapi=False, color_marker=False, opt=None):
     if not opt:
         opt = get_opt(model_path)
         #print_options(opt)
@@ -488,6 +489,63 @@ def inference(img, tile_size, overlap_size, model_path, use_torchserve=False, ea
         raise Exception(f'inference() not implemented for model {opt.model}')
 
 
+def inference(img, tile_size, overlap_size, model_path, use_torchserve=False,
+              eager_mode=False, color_dapi=False, color_marker=False, opt=None):
+    if not opt:
+        opt = get_opt(model_path)
+        #print_options(opt)
+
+    run_fn = run_torchserve if use_torchserve else run_dask
+
+    if opt.model == 'SDG':
+        # SDG could have multiple input images/modalities, hence the input could be a rectangle.
+        # We split the input to get each modality image then create tiles for each set of input images.
+        w, h = int(img.width / opt.input_no), img.height
+        orig = [img.crop((w * i, 0, w * (i+1), h)) for i in range(opt.input_no)]
+    else:
+        # Otherwise expect a single input image, which is used directly.
+        orig = img
+
+    tiler = InferenceTiler(orig, tile_size, overlap_size)
+    for tile in tiler:
+        tiler.stitch(run_wrapper(tile, run_fn, model_path, eager_mode, opt))
+    results = tiler.results()
+
+    if opt.model == 'DeepLIIF':
+        images = {
+            'Hema': results['G1'],
+            'DAPI': results['G2'],
+            'Lap2': results['G3'],
+            'Marker': results['G4'],
+            'Seg': results['G5'],
+        }
+        if color_dapi:
+            matrix = (       0,        0,        0, 0,
+                      299/1000, 587/1000, 114/1000, 0,
+                      299/1000, 587/1000, 114/1000, 0)
+            images['DAPI'] = images['DAPI'].convert('RGB', matrix)
+        if color_marker:
+            matrix = (299/1000, 587/1000, 114/1000, 0,
+                      299/1000, 587/1000, 114/1000, 0,
+                             0,        0,        0, 0)
+            images['Marker'] = images['Marker'].convert('RGB', matrix)
+        return images
+
+    elif opt.model == 'DeepLIIFExt':
+        images = {f'mod{i}': results[f'G_{i}'] for i in range(1, opt.modalities_no + 1)}
+        if opt.seg_gen:
+            images.update({f'Seg{i}': results[f'GS_{i}'] for i in range(1, opt.modalities_no + 1)})
+        return images
+
+    elif opt.model == 'SDG':
+        images = {f'mod{i}': results[f'G_{i}'] for i in range(1, opt.modalities_no + 1)}
+        return images
+
+    else:
+        #raise Exception(f'inference() not implemented for model {opt.model}')
+        return results # return result images with default key names (i.e., net names)
+
+
 def postprocess(orig, images, tile_size, model, seg_thresh=150, size_thresh='auto', marker_thresh='auto', size_thresh_upper=None):
     if model == 'DeepLIIF':
         resolution = '40x' if tile_size > 384 else ('20x' if tile_size > 192 else '10x')
@@ -545,7 +603,8 @@ def infer_modalities(img, tile_size, model_dir, eager_mode=False,
     images = inference(
         img,
         tile_size=tile_size,
-        overlap_size=compute_overlap(img_size, tile_size),
+        #overlap_size=compute_overlap(img_size, tile_size),
+        overlap_size=tile_size//16,
         model_path=model_dir,
         eager_mode=eager_mode,
         color_dapi=color_dapi,

{deepliif-1.1.10 → deepliif-1.1.11}/deepliif/util/__init__.py

@@ -118,6 +118,211 @@ def stitch_tile(img, tile, tile_size, overlap_size, i, j):
     img.paste(tile, (i * tile_size, j * tile_size))
 
 
+class InferenceTiler:
+    """
+    Iterable class to tile image(s) and stitch result tiles together.
+
+    To perform inference on a large image, that image will need to be
+    tiled into smaller tiles that can be run individually and then
+    stitched back together. This class wraps the functionality as an
+    iterable object that can accept a single image or list of images
+    if multiple images are taken as input for inference.
+
+    An overlap size can be specified so that neighboring tiles will
+    overlap at the edges, helping to reduce seams or other artifacts
+    near the edge of a tile. Padding of a solid color around the
+    perimeter of the tile is also possible, if needed. The specified
+    tile size includes this overlap and pad sizes, so a tile size of
+    512 with an overlap size of 32 and pad size of 16 would have a
+    central area of 416 pixels that are stitched into the result image.
+
+    Example Usage
+    -------------
+    tiler = InferenceTiler(img, 512, 32)
+    for tile in tiler:
+        result_tiles = infer(tile)
+        tiler.stitch(result_tiles)
+    images = tiler.results()
+    """
+
+    def __init__(self, orig, tile_size, overlap_size=0, pad_size=0, pad_color=(255, 255, 255)):
+        """
+        Initialize for tiling an image or list of images.
+
+        Parameters
+        ----------
+        orig : Image | list(Image)
+            Original image or list of images to be tiled.
+        tile_size: int
+            Size (width and height) of the tiles to be generated.
+        overlap_size: int [default: 0]
+            Amount of overlap on each side of the tile.
+        pad_size: int [default: 0]
+            Amount of solid color padding around perimeter of tile.
+        pad_color: tuple(int, int, int) [default: (255,255,255)]
+            RGB color to use for padding.
+        """
+
+        if tile_size <= 0:
+            raise ValueError('InfereneTiler input tile_size must be positive and non-zero')
+        if overlap_size < 0:
+            raise ValueError('InfereneTiler input overlap_size must be positive or zero')
+        if pad_size < 0:
+            raise ValueError('InfereneTiler input pad_size must be positive or zero')
+
+        self.single_orig = not type(orig) is list
+        if self.single_orig:
+            orig = [orig]
+
+        for i in range(1, len(orig)):
+            if orig[i].size != orig[0].size:
+                raise ValueError('InferenceTiler input images do not have the same size.')
+        self.orig_width = orig[0].width
+        self.orig_height = orig[0].height
+
+        # patch size to extract from input image, which is then padded to tile size
+        patch_size = tile_size - (2 * pad_size)
+
+        # make sure width and height are both at least patch_size
+        if orig[0].width < patch_size:
+            for i in range(len(orig)):
+                while orig[i].width < patch_size:
+                    mirrored = ImageOps.mirror(orig[i])
+                    orig[i] = ImageOps.expand(orig[i], (0, 0, orig[i].width, 0))
+                    orig[i].paste(mirrored, (mirrored.width, 0))
+                orig[i] = orig[i].crop((0, 0, patch_size, orig[i].height))
+        if orig[0].height < patch_size:
+            for i in range(len(orig)):
+                while orig[i].height < patch_size:
+                    flipped = ImageOps.flip(orig[i])
+                    orig[i] = ImageOps.expand(orig[i], (0, 0, 0, orig[i].height))
+                    orig[i].paste(flipped, (0, flipped.height))
+                orig[i] = orig[i].crop((0, 0, orig[i].width, patch_size))
+        self.image_width = orig[0].width
+        self.image_height = orig[0].height
+
+        overlap_width = 0 if patch_size >= self.image_width else overlap_size
+        overlap_height = 0 if patch_size >= self.image_height else overlap_size
+        center_width = patch_size - (2 * overlap_width)
+        center_height = patch_size - (2 * overlap_height)
+        if center_width <= 0 or center_height <= 0:
+            raise ValueError('InferenceTiler combined overlap_size and pad_size are too large')
+
+        self.c0x = pad_size                               # crop offset for left of non-pad content in result tile
+        self.c0y = pad_size                               # crop offset for top of non-pad content in result tile
+        self.c1x = overlap_width + pad_size               # crop offset for left of center region in result tile
+        self.c1y = overlap_height + pad_size              # crop offset for top of center region in result tile
+        self.c2x = patch_size - overlap_width + pad_size  # crop offset for right of center region in result tile
+        self.c2y = patch_size - overlap_height + pad_size # crop offset for bottom of center region in result tile
+        self.c3x = patch_size + pad_size                  # crop offset for right of non-pad content in result tile
+        self.c3y = patch_size + pad_size                  # crop offset for bottom of non-pad content in result tile
+        self.p1x = overlap_width               # paste offset for left of center region w.r.t (x,y) coord
+        self.p1y = overlap_height              # paste offset for top of center region w.r.t (x,y) coord
+        self.p2x = patch_size - overlap_width  # paste offset for right of center region w.r.t (x,y) coord
+        self.p2y = patch_size - overlap_height # paste offset for bottom of center region w.r.t (x,y) coord
+
+        self.overlap_width = overlap_width
+        self.overlap_height = overlap_height
+        self.patch_size = patch_size
+        self.center_width = center_width
+        self.center_height = center_height
+
+        self.orig = orig
+        self.tile_size = tile_size
+        self.pad_size = pad_size
+        self.pad_color = pad_color
+        self.res = {}
+
+    def __iter__(self):
+        """
+        Generate the tiles as an iterable.
+
+        Tiles are created and iterated over from top left to bottom
+        right, going across the rows. The yielded tile(s) match the
+        type of the original input when initialized (either a single
+        image or a list of images in the same order as initialized).
+        The (x, y) coordinate of the current tile is maintained
+        internally for use in the stitch function.
+        """
+
+        for y in range(0, self.image_height, self.center_height):
+            for x in range(0, self.image_width, self.center_width):
+                if x + self.patch_size > self.image_width:
+                    x = self.image_width - self.patch_size
+                if y + self.patch_size > self.image_height:
+                    y = self.image_height - self.patch_size
+                self.x = x
+                self.y = y
+                tiles = [im.crop((x, y, x + self.patch_size, y + self.patch_size)) for im in self.orig]
+                if self.pad_size != 0:
+                    tiles = [ImageOps.expand(t, self.pad_size, self.pad_color) for t in tiles]
+                yield tiles[0] if self.single_orig else tiles
+
+    def stitch(self, result_tiles):
+        """
+        Stitch result tiles into the result images.
+
+        The key names for the dictionary of result tiles are used to
+        stitch each tile into its corresponding final image in the
+        results attribute. If a result image does not exist for a
+        result tile key name, then it will be created. The result tiles
+        are stitched at the location from which the list iterated tile
+        was extracted.
+
+        Parameters
+        ----------
+        result_tiles : dict(str: Image)
+            Dictionary of result tiles from the inference.
+        """
+
+        for k, tile in result_tiles.items():
+            if k not in self.res:
+                self.res[k] = Image.new('RGB', (self.image_width, self.image_height))
+            if tile.size != (self.tile_size, self.tile_size):
+                tile = tile.resize((self.tile_size, self.tile_size))
+            self.res[k].paste(tile.crop((self.c1x, self.c1y, self.c2x, self.c2y)), (self.x + self.p1x, self.y + self.p1y))
+
+            # top left corner
+            if self.x == 0 and self.y == 0:
+                self.res[k].paste(tile.crop((self.c0x, self.c0y, self.c1x, self.c1y)), (self.x, self.y))
+            # top row
+            if self.y == 0:
+                self.res[k].paste(tile.crop((self.c1x, self.c0y, self.c2x, self.c1y)), (self.x + self.p1x, self.y))
+            # top right corner
+            if self.x == self.image_width - self.patch_size and self.y == 0:
+                self.res[k].paste(tile.crop((self.c2x, self.c0y, self.c3x, self.c1y)), (self.x + self.p2x, self.y))
+            # left column
+            if self.x == 0:
+                self.res[k].paste(tile.crop((self.c0x, self.c1y, self.c1x, self.c2y)), (self.x, self.y + self.p1y))
+            # right column
+            if self.x == self.image_width - self.patch_size:
+                self.res[k].paste(tile.crop((self.c2x, self.c1y, self.c3x, self.c2y)), (self.x + self.p2x, self.y + self.p1y))
+            # bottom left corner
+            if self.x == 0 and self.y == self.image_height - self.patch_size:
+                self.res[k].paste(tile.crop((self.c0x, self.c2y, self.c1x, self.c3y)), (self.x, self.y + self.p2y))
+            # bottom row
+            if self.y == self.image_height - self.patch_size:
+                self.res[k].paste(tile.crop((self.c1x, self.c2y, self.c2x, self.c3y)), (self.x + self.p1x, self.y + self.p2y))
+            # bottom right corner
+            if self.x == self.image_width - self.patch_size and self.y == self.image_height - self.patch_size:
+                self.res[k].paste(tile.crop((self.c2x, self.c2y, self.c3x, self.c3y)), (self.x + self.p2x, self.y + self.p2y))
+
+    def results(self):
+        """
+        Return a dictionary of result images.
+
+        The keys for the result images are the same as those used for
+        the result tiles in the stitch function. This function should
+        only be called once, since the stitched images will be cropped
+        if the original image size was less than the patch size.
+        """
+
+        if self.orig_width != self.image_width or self.orig_height != self.image_height:
+            return {k: im.crop((0, 0, self.orig_width, self.orig_height)) for k, im in self.res.items()}
+        else:
+            return {k: im for k, im in self.res.items()}
+
+
 def calculate_background_mean_value(img):
     img = cv2.fastNlMeansDenoisingColored(np.array(img), None, 10, 10, 7, 21)
     img = np.array(img, dtype=float)

{deepliif-1.1.10 → deepliif-1.1.11/deepliif.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.10
+Version: 1.1.11
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -24,6 +24,8 @@ License-File: LICENSE.md
     |
     <a href="https://onlinelibrary.wiley.com/share/author/4AEBAGEHSZE9GDP3H8MN?target=10.1111/his.15048">Histopathology'23</a>
     |
+    <a href="https://arxiv.org/abs/2405.08169">MICCAI'24</a>
+    |
     <a href="https://deepliif.org/">Cloud Deployment</a>
     |
     <a href="https://nadeemlab.github.io/DeepLIIF/">Documentation</a>
@@ -250,7 +252,7 @@ The plugin also supports submitting multiple ROIs at once:
 ## Cloud Deployment
 If you don't have access to GPU or appropriate hardware and don't want to install ImageJ, we have also created a [cloud-native DeepLIIF deployment](https://deepliif.org) with a user-friendly interface to upload images, visualize, interact, and download the final results.
 
-![DeepLIIF Website Demo](images/deepliif-website-demo-03.gif)
+![DeepLIIF Website Demo](images/deepliif-website-demo-04.gif)
 
 ## Cloud API Endpoints
 
@@ -549,4 +551,11 @@ If you find our work useful in your research or if you use parts of this code or
   year = {2023},
   doi = {https://doi.org/10.1111/his.15048}
 }
+
+@article{zehra2024deepliifstitch,
+author = {Zehra, Talat and Marino, Joseph and Wang, Wendy and Frantsuzov, Grigoriy and Nadeem, Saad},
+title = {Rethinking Histology Slide Digitization Workflows for Low-Resource Settings},
+journal = {International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
+year = {2024}
+}
 ```

{deepliif-1.1.10 → deepliif-1.1.11}/setup.cfg

@@ -3,7 +3,7 @@ name = deepliif
 description_file = README.md
 author = Parmida93
 author_email = ghahremani.parmida@gmail.com
-version = 1.1.10
+version = 1.1.11
 url = https://github.com/nadeemlab/DeepLIIF
 
 [egg_info]

{deepliif-1.1.10 → deepliif-1.1.11}/setup.py

@@ -6,7 +6,7 @@ README = (HERE / "README.md").read_text()
 
 setup(
     name='deepliif',
-    version='1.1.10',
+    version='1.1.11',
     packages=['deepliif', 'deepliif.data', 'deepliif.models', 'deepliif.util', 'deepliif.options'],
 
     description='DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification',