From 2815656944a0b332ea2410c3f600b087e15b9639 Mon Sep 17 00:00:00 2001
From: tpollina <thibaut.pollina@gmail.com>
Date: Thu, 16 Jan 2020 16:19:03 +0100
Subject: [PATCH] Create morphocut.py

---
 morphocut/morphocut.py | 116 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 morphocut/morphocut.py

diff --git a/morphocut/morphocut.py b/morphocut/morphocut.py
new file mode 100644
index 0000000..2fbd9f3
--- /dev/null
+++ b/morphocut/morphocut.py
@@ -0,0 +1,116 @@
+"""Experiment on processing KOSMOS data using MorphoCut."""
+
+import datetime
+import os
+
+from skimage.util import img_as_ubyte
+
+from morphocut import Call
+from morphocut.contrib.ecotaxa import EcotaxaWriter
+from morphocut.contrib.zooprocess import CalculateZooProcessFeatures
+from morphocut.core import Pipeline
+from morphocut.file import Find
+from morphocut.image import (
+    ExtractROI,
+    FindRegions,
+    ImageReader,
+    ImageWriter,
+    RescaleIntensity,
+    RGB2Gray,
+)
+from morphocut.stat import RunningMedian
+from morphocut.str import Format
+from morphocut.stream import TQDM, Enumerate
+
+# import_path = "/data-ssd/mschroeder/Datasets/Pyrocystis_noctiluca/RAW"
+import_path = "/home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/afternoon/14_1"
+export_path = "/home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/14_1_export"
+archive_fn = os.path.join(export_path, "14_1_morphocut_processed.zip")
+
+# Meta data that is added to every object
+global_metadata = {
+    "acq_instrument": "Planktoscope",
+    "process_datetime": datetime.datetime.now(),
+}
+
+if __name__ == "__main__":
+    print("Processing images under {}...".format(import_path))
+
+    # Create export_path in case it doesn't exist
+    os.makedirs(export_path, exist_ok=True)
+
+    # Define processing pipeline
+    with Pipeline() as p:
+        # Recursively find .jpg files in import_path.
+        # Sort to get consective frames.
+        abs_path = Find(import_path, [".jpg"], sort=True, verbose=True)
+
+        # Extract name from abs_path
+        name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
+
+        # Read image
+        img = ImageReader(abs_path)
+
+        # Apply running median to approximate the background image
+        flat_field = RunningMedian(img, 10)
+
+        # Correct image
+        img = img / flat_field
+
+        # Rescale intensities and convert to uint8 to speed up calculations
+        img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
+
+        # Show progress bar for frames
+        TQDM(Format("Frame {name}", name=name))
+
+        # Convert image to uint8 gray
+        img_gray = RGB2Gray(img)
+        img_gray = Call(img_as_ubyte, img_gray)
+
+        # Apply threshold find objects
+        threshold = 204  # Call(skimage.filters.threshold_otsu, img_gray)
+        mask = img_gray < threshold
+
+        # Write corrected frames
+        frame_fn = Format(os.path.join(export_path, "{name}.jpg"), name=name)
+        ImageWriter(frame_fn, img)
+
+        # Find objects
+        regionprops = FindRegions(
+            mask, img_gray, min_area=100, padding=10, warn_empty=name
+        )
+
+        # For an object, extract a vignette/ROI from the image
+        roi_orig = ExtractROI(img, regionprops, bg_color=255)
+        roi_gray = ExtractROI(img_gray, regionprops, bg_color=255)
+
+        # Generate an object identifier
+        i = Enumerate()
+        object_id = Format("{name}_{i:d}", name=name, i=i)
+
+        # Calculate features. The calculated features are added to the global_metadata.
+        # Returns a Variable representing a dict for every object in the stream.
+        meta = CalculateZooProcessFeatures(
+            regionprops, prefix="object_", meta=global_metadata
+        )
+        # If CalculateZooProcessFeatures is not used, we need to copy global_metadata into the stream:
+        # meta = Call(lambda: global_metadata.copy())
+        # https://github.com/morphocut/morphocut/issues/51
+
+        # Add object_id to the metadata dictionary
+        meta["object_id"] = object_id
+
+        # Generate object filenames
+        orig_fn = Format("{object_id}.jpg", object_id=object_id)
+        gray_fn = Format("{object_id}-gray.jpg", object_id=object_id)
+
+        # Write objects to an EcoTaxa archive:
+        # roi image in original color, roi image in grayscale, metadata associated with each object
+        EcotaxaWriter(archive_fn, [(orig_fn, roi_orig), (gray_fn, roi_gray)], meta)
+
+        # Progress bar for objects
+        TQDM(Format("Object {object_id}", object_id=object_id))
+
+    # Execute pipeline
+    p.run()
+