Clean up argument parsing

.gitignore

@@ -17,6 +17,6 @@ LAStools.zip
 pcl.tar.gz
 ceres-solver.tar.gz
 *.pyc
-pcl.tar.gz
 opencv.zip
-settings.yaml
+settings.yaml
+docker.settings.yaml

docker.settings.yaml

@@ -1,53 +1,49 @@
 ---
 # A list of global configuration variables
-# WARNING: DO NOT EDIT THIS FILE!!!
-# Copy this file and rename to settings.yaml to override. You can also place the a settings.yaml
-# file with the same format inside your project to more specific parameter needs.
+# Uncomment lines as needed to edit default settings.
 # Note this only works for settings with default values. Some commands like --rerun <module>
 # or --force-ccd n will have to be set in the command line (if you need to)
 
-settings:
-  # These are really important to set up properly
-  project_path: '/' # DO NOT CHANGE THIS
-  resize_to: 2400
-  start_with: 'resize'
-  end_with: 'odm_orthophoto'
-  rerun_all: False
-  zip_results: False
-  verbose: False
-  time: False
-  opensfm:
-    processes: 4 # IMPORTANT: Set this to nproc-1 or lower for larger datasets
-    min_num_features: 4000
-    matcher_threshold: 2.0
-    matcher_ratio: 0.6
-    matcher_neighbors: 8
-    matcher_distance: 0
-  pmvs: # The following settings only matter if use_pmvs is set to True
-    enabled: False
-    cmvs_max_images: 500
-    level: 1
-    cell_size: 2
-    threshold: 0.7
-    wsize: 7
-    min_images: 3
-    num_cores: 4 # Set this to nproc
-  mesh:
-    size: 100000
-    octree_depth: 9
-    samples: 1.0
-    solver_divide: 9
-  texturing:
-    data_term: 'gmi'
-    outlier_removal_type: 'gauss_clamping'
-    skip_visibility_test: False
-    skip_global_seam_leveling: False
-    skip_local_seam_leveling: False
-    skip_hole_filling: False
-    keep_unseen_faces: False
-    tone_mapping: 'none'
-  georeferencing:
-    gcp: !!null     # YAML tag for None
-    use_exif: False # Set to True if you have a GCP file (it auto-detects) and want to use EXIF
-  orthophoto:
-    resolution: 20.0 # Pixels/meter
+# This line is really important to set up properly
+project_path: '/' #DO NOT CHANGE THIS OR DOCKER WILL NOT WORK. It should be '/'
+
+# The rest of the settings will default to the values set unless you uncomment and change them
+#resize_to: 2400
+#start_with: 'resize'
+#end_with: 'odm_orthophoto'
+#rerun_all: False
+#zip_results: False
+#verbose: False
+#time: False
+#opensfm_processes: 4 # by default this is set to $(nproc)
+#min_num_features: 4000
+#matcher_threshold: 2.0
+#matcher_ratio: 0.6
+#matcher_neighbors: 8
+#matcher_distance: 0
+#use_pmvs: False # The cmvs/pmvs settings only matter if 'Enabled' is set to True
+#cmvs_maximages: 500
+#pmvs_level: 1
+#pmvs_csize: 2
+#pmvs_threshold: 0.7
+#pmvs_wsize: 7
+#pmvs_min_images: 3
+#pmvs_num_cores: 4 # by default this is set to $(nproc)
+#mesh_size: 100000
+#mesh_octree_depth: 9
+#mesh_samples: 1.0
+#mesh_solver_divide: 9
+#texturing_data_term: 'gmi'
+#texturing_outlier_removal_type: 'gauss_clamping'
+#texturing_skip_visibility_test: False
+#texturing_skip_global_seam_leveling: False
+#texturing_skip_local_seam_leveling: False
+#texturing_skip_hole_filling: False
+#texturing_keep_unseen_faces: False
+#texturing_tone_mapping: 'none'
+#gcp: !!null  # YAML tag for None
+#use_exif: False # Set to True if you have a GCP file (it auto-detects) and want to use EXIF
+#orthophoto_resolution: 20.0 # Pixels/meter
+#orthophoto_target_srs: !!null # Currently does nothing
+#orthophoto_no_tiled: False
+#orthophoto_compression: DEFLATE # Options are [JPEG, LZW, PACKBITS, DEFLATE, LZMA, NONE] Don't change unless you know what you are doing