Merge pull request #46 from AgPipeline/develop

Merging non-GeoTiff (plain tiff) support

Author: Chris-Schnaufer

README.md

@@ -67,11 +67,11 @@ Li, Zongyang, Abby Stylianou, and Robert Pless. "Learning to Correct for Bad Cam
 
 ### Sample Docker Command line
 
-First build the Docker image, using the Dockerfile, and tag it agdrone/transformer-soilmask:2.1. 
+First build the Docker image, using the Dockerfile, and tag it agdrone/transformer-soilmask:2.4. 
 Read about the [docker build](https://docs.docker.com/engine/reference/commandline/build/) command if needed.
 
 ```bash
-docker build -t agdrone/transformer-soilmask:2.1 ./
+docker build -t agdrone/transformer-soilmask:2.4 ./
 ```
 
 There are two files needed for running the Docker image.
@@ -89,11 +89,11 @@ 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=${PWD}/test_data,target=/mnt,type=bind" agdrone/transformer-soilmask:2.1 --working_space "/mnt" --metadata "/mnt/experiment.yaml" "/mnt/orthomosaic.tif"
+docker run --rm --mount "src=${PWD}/test_data,target=/mnt,type=bind" agdrone/transformer-soilmask:2.4 --working_space "/mnt" --metadata "/mnt/experiment.yaml" "/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:2.1`.
+The name of the image to run is `agdrone/transformer-soilmask:2.4`.
 
 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.

soilmask.py

@@ -385,7 +385,8 @@ def perform_process(self, environment: Environment, check_md: CheckMD, transform
         Return:
             Returns a dictionary with the results of processing
         """
-        # pylint: disable=unused-argument
+        # Disable pylint checks that negatively affect the code use and readability
+        # pylint: disable=unused-argument, too-many-branches
         result = {}
         file_md = []
 
@@ -401,17 +402,15 @@ def perform_process(self, environment: Environment, check_md: CheckMD, transform
                     continue
                 # 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:
                     rgb_mask_tif = environment.args.out_file
@@ -433,7 +432,10 @@ 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'],

tests/test_soilmask.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
@@ -129,3 +130,47 @@ def test_outputfile_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_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')
+    source_metadata = os.path.join(TESTING_FILE_PATH, 'experiment.yaml')
+    assert os.path.exists(source_image)
+    assert os.path.exists(source_metadata)
+
+    # 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, '--metadata', source_metadata, '--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)