errorhandling for v0.0.2 release

cyschneck · Mar 15, 2023 · 604e47c · 604e47c
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diff --git a/README.md b/README.md
@@ -4,15 +4,25 @@
 
 Find the centerline and width of rivers based on the latitude and longitude of the right and left bank
 
-| Points on River Bank | Centerline of River Bank |
+| River Outlined in ArcGIS | Generated Centerline for the River Bank |
 | ------------- | ------------- |
 | ![river_google_earth+png](https://raw.githubusercontent.com/cyschneck/centerline-width/main/data/doc_examples/river_example_google_earth.png) | ![river_centerline+png](https://raw.githubusercontent.com/cyschneck/centerline-width/main/data/doc_examples/river_example.png) |
 
 
 Python implementation of [R-Code CMGO](https://github.com/AntoniusGolly/cmgo) (with modification)
 
-## Data
-Scripts can accept a text file that can be converted to a .csv file
+## Requirements
+Currently running on Python 3.7+
+
+```
+pip install -r requirments.txt
+```
+
+## Running Script
+
+### Converted Data Text File to CSV
+
+Convert a text file with coordinates for a left and right bank's latitude/longitude
 
 ```
      llat       llon      rlat       rlon
@@ -21,29 +31,58 @@ Scripts can accept a text file that can be converted to a .csv file
 30.037648 -92.868546 30.119746 -92.907917
 30.037674 -92.868536 30.119721 -92.907909
 30.037702 -92.868533 30.119706 -92.907905
-...
 ```
 
-Scripts expect data as a list of point:
+Scripts expect data as a list of point for left and right banks:
 - Header: llat, llon, rlat, rlon
 
-## Requirements
-Currently running on Python 3.7+
-
 ```
-pip install -r requirments.txt
+convertColumnsToCSV(text_file=None, flipBankDirection=False)
 ```
-
-## Running Script
-
-### Converted Text File to CSV
+* **[REQUIRED]** text_file (string): File location of the text file to convert
+* [OPTIONAL] flipBankDirection (boolean): If the latitude/longitude of the banks are generated in reverse order, flip the final values so left/right bank are in order
 
 ```python
 import centerline_width
 centerline_width.convertColumnsToCSV(text_file="data/river_coords.txt", flipBankDirection=True)
 ```
+Converts text file:
+```
+     llat       llon      rlat       rlon
+30.037581 -92.868569 30.119804 -92.907933
+30.037613 -92.868549 30.119772 -92.907924
+30.037648 -92.868546 30.119746 -92.907917
+30.037674 -92.868536 30.119721 -92.907909
+30.037702 -92.868533 30.119706 -92.907905
+```
+To a CSV file:
+```
+llat,llon,rlat,rlon
+30.037581,-92.868569,30.037441,-92.867476
+30.037613,-92.868549,30.037448,-92.867474
+30.037648,-92.868546,30.037482,-92.867449
+30.037674,-92.868536,30.037506,-92.867432
+30.037702,-92.868533,30.037525,-92.867430
+```
 
 ### Plot Centerline in Matplotlib
+Plot the centerline created from a list of right and left banks with Voronoi vertices
+
+```
+plotCenterline(csv_data=None,
+			display_all_possible_paths=False, 
+			plot_title=None, 
+			save_plot_name=None, 
+			displayVoronoi=False, 
+			optional_cutoff=None)
+```
+* **[REQUIRED]** csv_data (string): File location of the text file to convert
+* [OPTIONAL] display_all_possible_paths (boolean): Display all possible paths, not just the centerline (useful for debugging)
+* [OPTIONAL] plot_title (string): Change plot title, defaults to "River Coordinates: Valid Centerline = True/False, Valid Polygon = True/False"
+* [OPTIONAL] save_plot_name (string): Save the plot with a given name and location
+* [OPTIONAL] displayVoronoi (boolean): Overlay Voronoi diagram used to generate centerline
+* [OPTIONAL] optional_cutoff (int): Include only the first x amount of the data to chart (useful for debugging)
+
 ```python
 import centerline_width
 centerline_width.plotCenterline(csv_data="data/river_coords.csv", 
@@ -56,12 +95,33 @@ Output:
 ![river_coords+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/river_coords.png)
 
 ### Return Latitude/Longitude Coordinates of Centerline
+Return a list of lists for each latitude/longtiude coordinate of the centerline
+```
+centerlineLatitudeLongitude(csv_data=None, optional_cutoff=None)
+```
+* **[REQUIRED]** csv_data (string): File location of the text file to convert
+* [OPTIONAL] optional_cutoff (int): Include only the first x amount of the data to chart (useful for debugging)
+
 ```python
 import centerline_width
 centerline_long_lat_coordinates = centerline_width.centerlineLatitudeLongitude(csv_data="data/river_coords.csv", 																optional_cutoff=cutoff)
 ```
 Output: `[(-92.86788596499872, 30.03786596717931), (-92.86789573751797, 30.037834641974108), (-92.8679141386283, 30.037789636848878), (-92.8679251193248, 30.037756853899904), (-92.86796903819089, 30.03765423778148), (-92.86797335733262, 30.037643336049054), (-92.8679920356456, 30.037592224469797), (-92.86800576063828, 30.037555441489403), (-92.86800841510367, 30.037546512833107), (-92.8680119498663, 30.03753043193875)]`
 ### Return Width of River
+Return the width of the river based on the centerline
+```
+riverWidthFromCenterline(csv_data=None,
+						centerline_coordinates=None,
+						save_to_csv=None,
+						optional_cutoff=None)
+```
+
+* **[REQUIRED]** csv_data (string): File location of the text file to convert
+* **[REQUIRED]** centerline_coordinates (list): A list of centerline coordinates (via centerlineLatitudeLongitude())
+* [OPTIONAL] plot_title (string): Change plot title, defaults to "River Coordinates: Valid Centerline = True/False, Valid Polygon = True/False"
+* [OPTIONAL] save_to_csv (string): Save the csv with a given name and location
+* [OPTIONAL] optional_cutoff (int): Include only the first x amount of the data to chart (useful for debugging)
+
 ```python
 import centerline_width
 river_width_dict = centerline_width.riverWidthFromCenterline(csv_data="data/river_coords.csv", 																centerline_coordinates=centerline_long_lat_coordinates,
@@ -84,38 +144,39 @@ The centerline is defined by the greatest distance from the right and left bank,
 ### Display Voronoi ridge vertices that lie within the polygon (within the river banks)
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example4.png)
 
-### Filter out any point pairs that only have one connections to filter out the short dead end paths
-
-###  Find the starting and ending node based on distance from the top and bottom of polygon
+### Filter out any point pairs that only have one connections to filter out the short dead end paths and find the starting and ending node based on distance from the top and bottom of polygon
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example6.png)
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example7.png)
 
-### Find the centerline: shortest path from the starting node to the ending node ([Dijkstra's Algorithm](https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html#networkx.algorithms.shortest_paths.generic.shortest_path))
+### Find the shortest path from the starting node to the ending node ([Dijkstra's Algorithm](https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html#networkx.algorithms.shortest_paths.generic.shortest_path))
 | Points on River Bank | NetworkX Graph of Points on River Bank |
 | ------------- | ------------- |
 | ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example10.png) | ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example9.png) |
 
+### Display the centerline found by connecting the starting/ending node with the shortest path
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example8.png)
 
 This is an attempt at a more robust algorithm working from raw data to ensure that all dead ends are removed and no gaps exist in the centerline
 
 Points that only have one connection are removed, but by limiting the number of connections for a point to just two will create gaps. The Voronoi vertices connect to other vertex values, but some connect to more and some only connect to one other point. Removing additional values will create gaps, so this is avoided in this code by not applying additional filters.
 
-All vertices:
+**All vertices:**
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example4.png)
 
-Vertices that have at least two connections (that would create gaps):
+**Vertices that have at least two connections (that would create gaps):**
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/example5.png)
 
-## Edge Cases
-Invalid Polygon
+## Debugging and Edge Cases
+A polygon is invalid if it overlaps within itself:
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/invalid_example1.png)
+In this example, the polygon is invalid, but with such a small overlap it is still able to find a valid path
 
-Invalid Polygon
+With limited data, the polygon will overlap more dramatically and will no longer be able to find a valid centerline:
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/invalid_example4.png)
 
-Invalid Starting Node
+If the data starts with a large width, it is possible for the starting node to be invalid
 ![example+png](https://raw.githubusercontent.com/cyschneck/river-geometry/main/data/doc_examples/invalid_example3.png)
+Currently, the starting node is determined by the closest node to the top of the bank (in green) and the ending node is determined by the closest node to the bottom of the bank (in red)
 
 ## Citations
 Based on the work:

diff --git a/centerline_width/error_handling.py b/centerline_width/error_handling.py
@@ -110,7 +110,7 @@ def errorHandlingRiverWidthFromCenterline(csv_data=None,
 				exit()
 
 	if type(centerline_coordinates) != list:
-		logger.critical("\nCRITICAL ERROR, [centerline_coordinates]: Must be a dict, current type = '{0}'".format(type(centerline_coordinates)))
+		logger.critical("\nCRITICAL ERROR, [centerline_coordinates]: Must be a list of lists, current type = '{0}'".format(type(centerline_coordinates)))
 		exit()
 
 	if save_to_csv is not None and type(save_to_csv) != str:

diff --git a/centerline_width/preprocessing.py b/centerline_width/preprocessing.py
@@ -74,6 +74,8 @@ def generatePolygon(left_bank_lst, right_bank_lst):
 
 	if not river_polygon.is_valid:
 		logger.critical("Invalid Polygon needs to be corrected")
+	else:
+		logger.info("Valid polygon generated")
 
 	return river_polygon, top_river, bottom_river
 
@@ -83,6 +85,7 @@ def generateVoronoi(left_bank_lst, right_bank_lst):
 	all_banks_points = np.array(all_banks_points)
 
 	river_voronoi = Voronoi(all_banks_points)
+	logger.info("Voronoi diagram generated")
 	return river_voronoi
 
 def pointsFromVoronoi(river_voronoi, river_polygon):

diff --git a/data/doc_examples/river_example_google_earth.png b/data/doc_examples/river_example_google_earth.png
diff --git a/data/river_coords.png b/data/river_coords.png
diff --git a/river_centerline_width_example.py b/river_centerline_width_example.py
@@ -6,21 +6,21 @@
 
 	# Valid Examples
 	cutoff = None
-	cutoff = 15 # valid centerline, valid path, valid polygon, valid starting node, valid ending node
+	#cutoff = 15 # valid centerline, valid path, valid polygon, valid starting node, valid ending node
 	#cutoff = 100 # valid centerline, valid path, valid polygon, valid starting node, valid ending node
-	#cutoff = 550 # valid centerline, valid path, valid polygon, valid starting node, valid ending node
+	cutoff = 550 # valid centerline, valid path, valid polygon, valid starting node, valid ending node
 	# Invalid Examples
 	#cutoff = 250 # valid centerline, valid path, invalid polygon, valid starting node, valid ending nodes
 	#cutoff = 40 # invalid centerline, valid path, valid polgyon, invalid starting node, valid ending node
 	#cutoff = 700 # invalid centerline, valid path, valid polgyon, invalid starting node, valid ending node
 	#cutoff = 1000 # invalid centerline, invalid path, invalid polgyon, invalid starting node, valid ending node
 
 	# Plot river banks
-	#centerline_width.plotCenterline(csv_data="data/river_coords.csv", 
-	#								save_plot_name="data/river_coords.png", 
-	#								display_all_possible_paths=True, 
-	#								displayVoronoi=False, 
-	#								optional_cutoff=cutoff)
+	centerline_width.plotCenterline(csv_data="data/river_coords.csv", 
+									save_plot_name="data/river_coords.png", 
+									display_all_possible_paths=True, 
+									displayVoronoi=False, 
+									optional_cutoff=cutoff)
 
 	# Return the latitude/longtiude coordinates for the centerline
 	centerline_long_lat_coordinates = centerline_width.centerlineLatitudeLongitude(csv_data="data/river_coords.csv", 
@@ -30,4 +30,5 @@
 	# Return the width of the river for each centerline vertex (distance from right, left, total)
 	river_width_dict = centerline_width.riverWidthFromCenterline(csv_data="data/river_coords.csv", 
 																centerline_coordinates=centerline_long_lat_coordinates,
-																save_to_csv="data/river_width.csv")
+																save_to_csv="data/river_width.csv",
+																optional_cutoff=cutoff)
diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 # Python Package Setup
 from setuptools import setup, find_namespace_packages
 
-VERSION="0.0.1"
+VERSION="0.0.2"
 DESCRIPTION="A Python package to find the centerline and width of rivers based on the latitude and longitude from a right and left bank"
 
 with open("README.md", "r") as f:
@@ -17,7 +17,7 @@
 	long_description_content_type='text/markdown',
 	url="https://github.com/cyschneck/centerline-width",
 	download_url="https://github.com/cyschneck/centerline-width/archive/refs/tags/v{0}.tar.gz".format(VERSION),
-	author="cyschneck (C. Y. Schneck)",
+	author="Una Schneck (unaschneck), C. Y. Schneck (cyschneck)",
 	keywords=["geophysics", "python", "voronoi", "centerline", "centerline-extraction", "river-bank", "limnology", "hydrology"],
 	license="MIT",
 	classifiers=[