Merge pull request #12 from AgPipeline/develop

Merging support for non-GeoTIFF images (plain TIFF)

README.md

@@ -33,7 +33,7 @@ First build the Docker image, using the Dockerfile, and tag it agdrone/transform
 Read about the [docker build](https://docs.docker.com/engine/reference/commandline/build/) command if needed.
 
 ```bash
-docker build -t agdrone/transformer-soilmask-by-ratio:1.0 ./
+docker build -t agdrone/transformer-soilmask-by-ratio:1.2 ./
 ```
 
 There is one file needed for running the Docker image.
@@ -50,11 +50,11 @@ An explanation of the command line options used follows.
 Be sure to read up on the [docker run](https://docs.docker.com/engine/reference/run/) command line for more information.
 
 ```bash
-docker run --rm --mount "src=${PWD}/test_data,target=/mnt,type=bind" agdrone/transformer-soilmask-by-ratio:1.0 --ratio 1.25 --working_space "/mnt" "/mnt/orthomosaic.tif"
+docker run --rm --mount "src=${PWD}/test_data,target=/mnt,type=bind" agdrone/transformer-soilmask-by-ratio:1.2 --ratio 1.25 --working_space "/mnt" "/mnt/orthomosaic.tif"
 ```
 
 This example command line assumes the source files are located in the `test_data` folder off the current folder.
-The name of the image to run is `agdrone/transformer-soilmask-by-ratio:1.0`.
+The name of the image to run is `agdrone/transformer-soilmask-by-ratio:1.2`.
 
 We are using the same folder for the source files and the output files.
 By using multiple `--mount` options, the source and output files can be separated.

tests/test_soilmask_ratio.py

@@ -6,6 +6,7 @@
 import json
 import subprocess
 import numpy as np
+import PIL.Image
 from osgeo import gdal
 
 # The name of the source file to test and it's path
@@ -155,3 +156,45 @@ def test_ratio_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_ratio_plain_tiff():
+    """Runs the command line for a non-GeoTiff file and tests the result"""
+    orthomosaic_mask_name = 'plain_mask.tif'
+    result_name = 'result.json'
+    source_image = os.path.join(TESTING_FILE_PATH, 'orthomosaic.tif')
+    assert os.path.exists(source_image)
+
+    # Create a non-georeferenced tiff image from the source image
+    plain_tiff_image = os.path.join(TESTING_FILE_PATH, 'plain.tif')
+    if os.path.exists(plain_tiff_image):
+        os.unlink(plain_tiff_image)
+    img = PIL.Image.open(source_image)
+    img_array = np.array(img)
+    result = PIL.Image.fromarray(img_array)
+    result.save(plain_tiff_image)
+
+    # Setup parameters for running the test
+    working_space = os.path.realpath('./test_results')
+    os.makedirs(working_space, exist_ok=True)
+    for expected_file in [result_name, orthomosaic_mask_name]:
+        cur_path = os.path.join(working_space, expected_file)
+        if os.path.exists(cur_path):
+            os.unlink(cur_path)
+
+    command_line = [SOURCE_PATH, '--working_space', working_space, plain_tiff_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)

transformer.py

@@ -204,7 +204,8 @@ def perform_process(self, environment: Environment, check_md: CheckMD, transform
         Return:
             Returns a dictionary with the results of processing
         """
-        # pylint: disable=unused-argument, no-self-use
+        # Disable pylint warnings that reduce readability
+        # pylint: disable=unused-argument, no-self-use, too-many-branches
         result = {}
         file_md = []
 
@@ -221,17 +222,14 @@ def perform_process(self, environment: Environment, check_md: CheckMD, transform
 
                 # Get the image's EPSG code
                 epsg = geoimage.get_epsg(one_file)
-                if epsg is None:
-                    logging.debug("Skipping image that is not georeferenced: '%s'", one_file)
-                    continue
+                if epsg is not None:
+                    # Get the bounds of the image to see if we can process it.
+                    bounds = geoimage.image_get_geobounds(one_file)
 
-                # Get the bounds of the image to see if we can process it.
-                bounds = geoimage.image_get_geobounds(one_file)
-
-                if bounds is None:
-                    logging.warning("Unable to get bounds of georeferenced image: '%s'",
-                                    os.path.basename(one_file))
-                    continue
+                    if bounds is None:
+                        logging.warning("Unable to get bounds of georeferenced image: '%s'",
+                                        os.path.basename(one_file))
+                        continue
 
                 # Get the mask name
                 if environment.args.out_file:
@@ -255,7 +253,10 @@ def perform_process(self, environment: Environment, check_md: CheckMD, transform
                 transformer_info = environment.generate_transformer_md()
 
                 image_md = __internal__.prepare_metadata_for_geotiff(transformer_info)
-                geoimage.create_geotiff(mask_rgb, bounds, rgb_mask_tif, epsg, None, False, image_md, compress=True)
+                if epsg:
+                    geoimage.create_geotiff(mask_rgb, bounds, rgb_mask_tif, epsg, None, False, image_md, compress=True)
+                else:
+                    geoimage.create_tiff(mask_rgb, rgb_mask_tif, None, False, image_md, compress=True)
 
                 transformer_md = {
                     'name': transformer_info['name'],