Merge pull request #25 from AgPipeline/update_info

Update info and adding output file command line option

README.md

@@ -105,7 +105,7 @@ The command line parameters after the image name are passed to the software insi
 Note that the paths provided are relative to the running image (see the --mount option specified above).
 
 - `--working_space "/mnt"` specifies the folder to use as a workspace
-- `--metadata "/mnt/experiment.yaml"` is the name of the source metadata to be cleaned
+- `--metadata "/mnt/experiment.yaml"` is the name of the source metadata
 - `"/mnt/orthomosaic.tif"` is the name of the image to mask
 
 ## Acceptance Testing

configuration.py

@@ -9,13 +9,13 @@ class ConfigurationSoilmask(Configuration):
     # pylint: disable=too-few-public-methods
 
     # The version number of the transformer
-    transformer_version = '2.0'
+    transformer_version = '2.2'
 
     # The transformer description
-    transformer_description = 'Stereo RGB Image Enhancement & Masking'
+    transformer_description = 'RGB Image Soil Masking'
 
     # Short name of the transformer
-    transformer_name = 'terra.stereo-rgb.rgbmask'
+    transformer_name = 'soilmask'
 
     # The name of the author of the extractor
     author_name = 'Chris Schnaufer'
@@ -24,7 +24,7 @@ class ConfigurationSoilmask(Configuration):
     author_email = '[email protected]'
 
     # Repository URI of where the source code lives
-    repository = 'https://github.com/Chris-Schnaufer/rgbmask.git'
+    repository = 'https://github.com/AgPipeline/transformer-soilmask'
 
     # Contributors to this transformer
     contributors = ['Max Burnette', 'Zongyang Li', 'Todd Nicholson']
@@ -33,4 +33,4 @@ class ConfigurationSoilmask(Configuration):
     transformer_sensor = 'stereoTop'
 
     # The transformer type (eg: 'rgbmask', 'plotclipper')
-    transformer_type = 'rgb_mask'
+    transformer_type = 'rgbmask'

soilmask.py

@@ -2,6 +2,7 @@
 """Soil masking Transformer
 """
 
+import argparse
 import logging
 import os
 import numpy as np
@@ -327,6 +328,16 @@ def supported_file_ext(self) -> tuple:
         """Returns a tuple of supported file extensions in lowercase (with the preceeding dot: eg '.tif')"""
         return '.tiff', '.tif'
 
+    def add_parameters(self, parser: argparse.ArgumentParser) -> None:
+        """Adds parameters
+        Arguments:
+            parser: instance of argparse
+        """
+        # pylint: disable=no-self-use
+        parser.add_argument('--out_file', type=str, help='the path to save the masked file to')
+
+        parser.epilog += '  Mask files are saved with the .msk filename extension added when not specified.'
+
     def check_continue(self, environment: Environment, check_md: dict, transformer_md: list,
                        full_md: list) -> tuple:
         """Checks if conditions are right for continuing processing
@@ -402,8 +413,14 @@ def perform_process(self, environment: Environment, check_md: dict, transformer_
                                     os.path.basename(one_file))
                     continue
 
-                # Get the mask name using the original name as reference
-                rgb_mask_tif = os.path.join(check_md['working_folder'], __internal__.get_maskfilename(one_file))
+                # Get the mask name
+                if environment.args.out_file:
+                    rgb_mask_tif = environment.args.out_file
+                    if not os.path.dirname(rgb_mask_tif):
+                        rgb_mask_tif = os.path.join(check_md['working_folder'], rgb_mask_tif)
+                else:
+                    # Use the original name
+                    rgb_mask_tif = os.path.join(check_md['working_folder'], __internal__.get_maskfilename(one_file))
 
                 # Create the mask file
                 logging.debug("Creating mask file '%s'", rgb_mask_tif)

tests/test_soilmask.py

@@ -70,7 +70,7 @@ def test_prepare_metadata_for_geotiff():
                             assert value == str(test[METADATA_KEY_TRANSLATION['transformer_repo']]['repUrl'])
 
 
-def test_command_line():
+def test_simple_line():
     """Runs the command line and tests the result"""
     orthomosaic_mask_name = 'orthomosaic_mask.tif'
     result_name = 'result.json'
@@ -98,3 +98,34 @@ def test_command_line():
     img = gdal.Open(os.path.join(working_space, orthomosaic_mask_name)).ReadAsArray()
     assert img is not None
     assert isinstance(img, np.ndarray)
+
+
+def test_outputfile_command_line():
+    """Runs the command line and tests the result"""
+    orthomosaic_mask_name = 'soilmask.tif'
+    result_name = 'result.json'
+    source_image = os.path.join(TESTING_FILE_PATH, 'orthomosaic.tif')
+    source_metadata = os.path.join(TESTING_FILE_PATH, 'experiment.yaml')
+    assert os.path.exists(source_image)
+    assert os.path.exists(source_metadata)
+
+    working_space = os.path.realpath('./test_results')
+    os.makedirs(working_space, exist_ok=True)
+
+    command_line = [SOURCE_PATH, '--metadata', source_metadata, '--working_space', working_space,
+                    '--out_file', orthomosaic_mask_name, source_image]
+    subprocess.run(command_line, check=True)
+
+    # Check that the expected files were created
+    for expected_file in [result_name, orthomosaic_mask_name]:
+        assert os.path.exists(os.path.join(working_space, expected_file))
+
+    # Inspect the created files
+    with open(os.path.join(working_space, result_name)) as in_file:
+        res = json.load(in_file)
+        assert 'code' in res
+        assert res['code'] == 0
+
+    img = gdal.Open(os.path.join(working_space, orthomosaic_mask_name)).ReadAsArray()
+    assert img is not None
+    assert isinstance(img, np.ndarray)