Upload example of transforming raw MERFISH -> spaceTx formatted data

examples/get_merfish_u20s_data.py

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+import argparse
+import io
+import os
+from typing import IO, Tuple
+
+from skimage.io import imread, imsave
+from slicedimage import ImageFormat
+
+from starfish.experiment.builder import FetchedTile, TileFetcher, write_experiment_json
+from starfish.types import Indices
+from starfish.util.argparse import FsExistsType
+
+SHAPE = 2048, 2048
+
+
+class MERFISHTile(FetchedTile):
+    def __init__(self, file_path, hyb, ch):
+        self.file_path = file_path
+        # how to index tiles from indices into multi-page tiff
+        # key is a tuple of round, chan. val is the index
+        self.map = {(0, 0): 0,
+                    (0, 1): 1,
+                    (1, 0): 3,
+                    (1, 1): 2,
+                    (2, 0): 4,
+                    (2, 1): 5,
+                    (3, 0): 6,
+                    (3, 1): 7,
+                    (4, 0): 9,
+                    (4, 1): 8,
+                    (5, 0): 10,
+                    (5, 1): 11,
+                    (6, 0): 12,
+                    (6, 1): 13,
+                    (7, 0): 15,
+                    (7, 1): 14}
+        self.hyb = hyb
+        self.ch = ch
+
+    @property
+    def shape(self) -> Tuple[int, ...]:
+        return SHAPE
+
+    @property
+    def format(self) -> ImageFormat:
+        return ImageFormat.TIFF
+
+    def tile_data_handle(self) -> IO:
+        im = imread(self.file_path)
+        im = im[self.map[(self.hyb, self.ch)], :, :]
+        fh = io.BytesIO()
+        imsave(fh, im, plugin='tifffile')
+        fh.seek(0)
+        return fh
+
+
+class MERFISHAuxTile(FetchedTile):
+    def __init__(self, file_path):
+        self.file_path = file_path
+        self.dapi_index = 17
+
+    @property
+    def shape(self) -> Tuple[int, ...]:
+        return SHAPE
+
+    @property
+    def format(self) -> ImageFormat:
+        return ImageFormat.TIFF
+
+    def tile_data_handle(self) -> IO:
+        im = imread(self.file_path)[self.dapi_index, :, :]
+        fh = io.BytesIO()
+        imsave(fh, im, plugin='tifffile')
+        fh.seek(0)
+        return fh
+
+
+class MERFISHTileFetcher(TileFetcher):
+    def __init__(self, input_dir, is_dapi):
+        self.input_dir = input_dir
+        self.is_dapi = is_dapi
+
+    def get_tile(self, fov: int, hyb: int, ch: int, z: int) -> FetchedTile:
+        filename = os.path.join(self.input_dir, 'fov_{}.tif'.format(fov))
+        file_path = os.path.join(self.input_dir, filename)
+        if self.is_dapi:
+            return MERFISHAuxTile(file_path)
+        else:
+            return MERFISHTile(file_path, hyb, ch)
+
+
+def format_data(input_dir, output_dir):
+    def add_codebook(experiment_json_doc):
+        experiment_json_doc['codebook'] = "codebook.json"
+        return experiment_json_doc
+
+    num_fovs = 1
+
+    hyb_dimensions = {
+        Indices.ROUND: 8,
+        Indices.CH: 2,
+        Indices.Z: 1,
+    }
+
+    aux_name_to_dimensions = {
+        'nuclei': {
+            Indices.ROUND: 1,
+            Indices.CH: 1,
+            Indices.Z: 1
+        }
+    }
+
+    write_experiment_json(output_dir,
+                          num_fovs,
+                          hyb_dimensions,
+                          aux_name_to_dimensions,
+                          primary_tile_fetcher=MERFISHTileFetcher(input_dir, is_dapi=False),
+                          aux_tile_fetcher={
+                              'nuclei': MERFISHTileFetcher(input_dir, is_dapi=True),
+                          },
+                          postprocess_func=add_codebook,
+                          default_shape=SHAPE
+                          )
+
+
+if __name__ == "__main__":
+    s3_bucket = "s3://czi.starfish.data.public/browse/raw/20180820/merfish_u2os/"
+    input_help_msg = "Path to raw data. Raw data can be downloaded from: {}".format(s3_bucket)
+    output_help_msg = "Path to output experment.json and all formatted images it references"
+    parser = argparse.ArgumentParser()
+    parser.add_argument("input_dir", type=FsExistsType(), help=input_help_msg)
+    parser.add_argument("output_dir", type=FsExistsType(), help=output_help_msg)
+
+    args = parser.parse_args()
+    format_data(args.input_dir, args.output_dir)