add "thermal" mode to readimage()

docs/read_image.md

@@ -8,7 +8,7 @@ Reads image into numpy ndarray and splits the path and image filename (*see note
 
 - **Parameters:**
     - filename - image file to be read (possibly including a path)
-    - mode     - return mode of image ("native," "rgb", "rgba", "csv", "envi", "arcgis", "gray", or "nd2"), defaults to "native"
+    - mode     - return mode of image ("native," "rgb", "rgba", "csv", "envi", "arcgis", "gray", "nd2", or "thermal"), defaults to "native"
 
 - **Context:**
     - Reads in file to be processed
@@ -18,7 +18,8 @@ Reads image into numpy ndarray and splits the path and image filename (*see note
     default settings (`mode="native"`). However, if the alpha channel is needed users must specify `mode="rgba"`. 
     - Comma separated data can be read in with `mode="csv"` so that, for example, thermal data can 
     be used in downstream analysis, such as [`pcv.analyze.thermal`](analyze_thermal.md).
-    - Nikon microscope images can be read in using `mode="nd2"`. 
+    - Nikon microscope images can be read in using `mode="nd2"`.
+    - FLIR thermal images can be read in using `mode="thermal"`. 
     - Hyperspectral data can be read in with `mode="envi"` where the filename parameter is the raw data file. There is also support for 
     ArcGis style hyperspectral images (`mode="arcgis"`). These modes of 
     reading in data expects a `filename`.hdr file which gets used for shaping the hyperspectral datacube and labeling bands of data

environment.yml

@@ -26,6 +26,7 @@ dependencies:
   - altair
   - vl-convert-python
   - git
+  - flyr
 
 channels:
   - conda-forge

plantcv/plantcv/readimage.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pandas as pd
 import nd2
+import flyr
 from plantcv.plantcv import fatal_error
 from plantcv.plantcv import params
 from plantcv.plantcv.hyperspectral import read_data
@@ -16,7 +17,7 @@ def readimage(filename, mode="native"):
 
     Inputs:
     filename = name of image file
-    mode     = mode of imread ("native", "rgb", "rgba", "gray", "csv", "envi", "arcgis", "nd2")
+    mode     = mode of imread ("native", "rgb", "rgba", "gray", "csv", "envi", "arcgis", "nd2", "thermal")
 
     Returns:
     img      = image object as numpy array
@@ -43,6 +44,8 @@ def readimage(filename, mode="native"):
         return array_data
     elif mode.upper() == "ND2":
         img = nd2.imread(filename)
+    elif mode.upper() == "THERMAL":
+        img = flyr.unpack(filename).celsius
     else:
         img = cv2.imread(filename, -1)
 

pyproject.toml

@@ -26,7 +26,8 @@ dependencies = [
     "statsmodels",
     "altair",
     "vl-convert-python",
-    "nd2"
+    "nd2",
+    "flyr"
 ]
 requires-python = ">=3.8"
 authors = [

tests/conftest.py

@@ -88,6 +88,8 @@ def __init__(self):
         self.kmeans_classifier_gray_dir = os.path.join(self.datadir, "kmeans_classifier_gray_dir")
         # nd2 file
         self.nd2_img = os.path.join(self.datadir, "test_nd2_img.nd2")
+        # flir thermal img
+        self.flir_img = os.path.join(self.datadir, "FLIR_test.jpg")
 
     @staticmethod
     def load_hsi(pkl_file):

tests/plantcv/test_readimage.py

@@ -51,6 +51,12 @@ def test_readimage_nd2(test_data):
     assert len(img.shape) == 3
 
 
+def test_readimage_thermal(test_data):
+    """Test for PlantCV."""
+    img, _, _ = readimage(filename=test_data.flir_img, mode="thermal")
+    assert len(img.shape) == 2
+
+
 def test_readimage_bad_file():
     """Test for PlantCV."""
     with pytest.raises(RuntimeError):