Merge pull request #30 from AgPipeline/alpha_channel

Alpha channel support

canopycover.py

@@ -198,12 +198,8 @@ def calculate_canopycover_masked(pxarray: np.ndarray) -> float:
     Notes:
         From TERRA REF canopy cover: https://github.com/terraref/extractors-stereo-rgb/tree/master/canopycover
     """
-    # If > 75% is NoData, return a -1 ccvalue for omission later
     total_size = pxarray.shape[0] * pxarray.shape[1]
     nodata = np.count_nonzero(pxarray[:, :, 3] == 0)
-    nodata_ratio = nodata/float(total_size)
-    if nodata_ratio > 0.75:
-        return -1
 
     # For masked images, all pixels with rgb>0,0,0 are considered canopy
     data = pxarray[pxarray[:, :, 3] == 255]
@@ -356,8 +352,6 @@ def perform_process(self, environment: Environment, check_md: dict, transformer_
                         else:
                             logging.info('Adding missing alpha channel to loaded image from "%s"', one_file)
                             image_to_use = _add_image_mask(one_file)
-#                            mask = np.where(np.sum(pxarray, axis=0) == 0, 0, 255).astype(pxarray.dtype)
-#                            image_to_use = np.stack((pxarray[0], pxarray[1], pxarray[2], mask))
                             del pxarray     # Potentially free up memory
 
                         logging.debug("Calculating canopy cover")
@@ -389,6 +383,8 @@ def perform_process(self, environment: Environment, check_md: dict, transformer_
                     else:
                         continue
                 except Exception as ex:
+                    if logging.getLogger().level == logging.DEBUG:
+                        logging.exception("Exception caught while processing canopy")
                     logging.warning("Exception caught while processing canopy cover: %s", str(ex))
                     logging.warning("Error generating canopy cover for '%s'", one_file)
                     logging.warning("    plot name: '%s'", plot_name)
@@ -398,7 +394,7 @@ def perform_process(self, environment: Environment, check_md: dict, transformer_
         if not num_files:
             return {'code': -1000, 'error': "No files were processed"}
         if not total_plots_calculated:
-            return {'code': -1001, 'error': "No plots intersected with the images provided"}
+            return {'code': -1001, 'error': "No images were able to have their canopy cover calculated"}
 
         # Setup the metadata for returning files
         file_md = []

tests/test_canopy_cover.py

@@ -9,7 +9,9 @@
 import os
 import random
 import re
+import shutil
 import string
+import tempfile
 from shutil import rmtree
 from subprocess import getstatusoutput
 #import pytest
@@ -53,15 +55,17 @@ def test_no_args():
     changed to some non-zero value to indicate a failure.
     """
     ret_val, out = getstatusoutput(SOURCE_PATH)
-    assert ret_val == 0
-    assert re.search('{}', out)
+    assert ret_val == 1
+    assert re.search('FileNotFoundError', out)
 
 
 def test_no_metadata():
     """ Run with a file but no metadata"""
-    ret_val, out = getstatusoutput(f'{SOURCE_PATH} {INPUT1}')
+    temp_dir = tempfile.mkdtemp()
+    ret_val, out = getstatusoutput(f'{SOURCE_PATH} --working_space {temp_dir}  {INPUT1}')
+    shutil.rmtree(temp_dir)
     assert ret_val == 0
-    assert re.search('{}', out)
+    assert re.search('"code": 0', out)
 
 
 def test_get_fields():