Oregon_Geologic_Map_Demo.py

'''
This script builds a geologic map of Oregon using an existing shapefile

Data source website: https://mrdata.usgs.gov/geology/state/state.php?state=OR
Shapefile source: http://pubs.usgs.gov/of/2005/1305/data/ORgeol_dd.zip
Color info file (right-click and "save page as"): https://mrdata.usgs.gov/catalog/lithrgb.txt

Setup instructions:
1) To run this script as-is, you will need to change the main_dir variable to reflect your desired path. 
2) You will need to create some folders at the destination, specifically a "Oregon_Geologic_Map_Demo" folder, and within it the "Methods", "Data", and "Results" folders.
You can either do that manually or run this script once from anywhere to automatically create them. 
3) Once you have created them, move the unzipped shapefile folder titled ORgeol_dd to the Data folder, as well as the color info file.
4) Now, save this script to the Methods folder and run it from there, if you wish.

Data files that are generated by this script will save to the Data folder, and the resulting map will save to Results
'''

import os
import re
import geopandas as gpd  
import pandas as pd
import numpy as np
import pygmt


# Controls whether the project folders data are automatically created
create_folders = True

# Controls whether the shapefile data is conditioned
condition_shp = True
    
# Controls whether a color palette table is made
create_cpt = True

# Controls whether a geologic unit legend postscript file is created
create_legend = True

# Controls whether the geologic map is created
plot_map = True


# Class that holds all the functions pretaining to creating a geologic map of Oregon
class Map_Maker():


    # Startup that runs each time the class is called
    def Create_Folders(self):

        # Main directory path
        self.main_dir = r'C:\Users\USER\Desktop\Oregon_Geologic_Map_Demo'

        # Path to the directory holding the project data files
        data_folder = os.path.join(self.main_dir, 'Data')

        # Path to the directory holding the project Python scripts
        methods_folder = os.path.join(self.main_dir, 'Methods')

        # Path to the directory holding the map generated by the scripts
        results_folder = os.path.join(self.main_dir, 'Results')

        # Path to the directory holding the conditioned shapefile data
        conditioned_shapefiles_folder = os.path.join(self.main_dir, 'Data', 'Conditioned_SHP')

        directories = [self.main_dir, data_folder, methods_folder, results_folder, conditioned_shapefiles_folder]

        # Iterates through the list of directories and creates them if they don't already exist
        for directory in directories:
            os.makedirs(directory, exist_ok = True)
        
        print("Be sure to set the create_folders parameter to False in order to run the main script")
        exit()

    

    # List that holds the inital unit names
    unit_names_list = []

    # Conditions the shapefile
    def Condition_Shapefile(self):
        
        # Shapefile of geologic unit polygons
        geo_polygons = os.path.join(self.main_dir, 'Data', 'ORgeol_dd', 'orgeol_poly_dd.shp')

        # Reads the shapefiel into a DataFrame
        df_geo_polygons = gpd.read_file(geo_polygons, driver = 'SHP')

        # Creates a numpy aray of the unique values in the ROCKTYPE1 column
        unit_names = df_geo_polygons['ROCKTYPE1'].unique()

        # List of unit names as they initally appear in the shapefile
        self.unit_names_list = list(unit_names)

        # Copy of unit names that is to be conditioned and subsituted for the original names
        conditioned_unit_names = list(unit_names)

        # Index of each character as they are read
        index = -1

        # Keys are what need to be replaced in words, and values are what they will be replaced with
        replacements = {' ':'_', '/':'_', '-':'_', '(':'_', ')':'_', 'é':'e', 'mã©lange':'melange'}

        # Iterates through the list of unique geologic unit names from the ROCKTYPE1 column and conditions them to the desired format
        for name in conditioned_unit_names:
            index += 1
            for old_value, new_value in replacements.items():
                if old_value in name:
                    conditioned_unit_names[index] = name.lower().replace(old_value, new_value)\

        # Replaces the geologic unit names of the ROCKTYPE1 column in the dataframe with the conditioned names
        for name, conditioned_name in zip(unit_names, conditioned_unit_names):
            df_geo_polygons['ROCKTYPE1'] = df_geo_polygons['ROCKTYPE1'].replace(name, conditioned_name)

        # Save name for the conditioned shapefile
        geo_polygons_conditioned = os.path.join(self.main_dir,'Data', 'Conditioned_SHP', 'OR_geology_polygons_CONDITIONED.shp')

        # Saves the DataFrame as an ESRI shapefile
        df_geo_polygons.to_file(geo_polygons_conditioned, driver = 'ESRI Shapefile')



    # Dictionary that holds the unit names from the cpt-like file prior to conditioning and the conditioned rgb colors
    cpt_data_dictionary = {}

    # Creates a color palette table file
    def Create_Color_Palette_Table(self):
        
        # Path to table of geologic unit colors
        geo_colors = os.path.join(self.main_dir, 'Data', 'lithrgb.txt')

        # Reads the table to a DataFrame, ignoring the "code" column and skipping the column names
        df_geo_colors = pd.read_csv(geo_colors, sep ='\t', usecols = [1,2,3,4], skiprows = 1, header = None)

        # Moves the geologic unit names column to be first
        df_geo_colors.set_index(df_geo_colors.columns[-1], inplace = True)

        # Resets the index so that the new column order is respected
        df_geo_colors.reset_index(inplace = True)

        # Save name for the new cpt
        geo_cpt = os.path.join(self.main_dir, 'Data', 'geology_color_palette.cpt')

        # Writes the DataFrame as a CSV file so that the data can be conditioned
        df_geo_colors.to_csv(geo_cpt, sep = '\t', header = None, index = False)

        with open(geo_cpt, 'r', encoding = 'latin-1') as f:
            data = f.read()

        # Keys are what need to be replaced in words, and values are what they will be replaced with
        replacements = {' ':'', '/':'_', '-':'_', '(':'_', ')':'_', 'é':'e', 'mã©lange':'melange'}

        # Iterates over the replacments dictionary and replaces the desired characters in the text
        for old_value, new_value in replacements.items():
            data = data.replace(old_value, new_value)

        # Converts the text to lowercase
        data = data.lower()

        # Regular expression that finds tab-spaces between numbers
        pattern = re.compile(r'(?<=\d)(\t)(?=\d)')

        # Uses the regular expression to replace tab-spaces with "/"
        data = pattern.sub('/', data)

        with open(geo_cpt, 'w') as f:
            f.write(data)

        # DataFrame used to hold the unit names from the cpt-like file prior to conditioning and the conditioned rgb colors
        self.df_cpt_data = pd.DataFrame()

        # Adds only the first column (unit name column) to a column in the new dataframe titled 'geo_unit'
        self.df_cpt_data['geo_unit'] = df_geo_colors.iloc[:, 0]

        # Reads in the conditioned cpt file using tab delimiters and no column titles
        df_cpt_data = pd.read_csv(geo_cpt, sep ='\t', header = None, encoding = 'latin-1')

        # Adds only the second column (unit color column) to a column in the new dataframe titled 'color'
        self.df_cpt_data['color'] = df_cpt_data.iloc[:, 1]

        # Converts the values of the 'geo_unit' and 'color' columns into a dictionary with 'geo_unit' as the key and 'color' as the value
        self.cpt_data_dictionary = pd.Series(self.df_cpt_data.color.values, index=self.df_cpt_data.geo_unit).to_dict()



    # Creates a legend postscript file
    def Create_Legend(self):
        
        # File path to the geologic unit legend postscript file
        geo_legend = os.path.join(self.main_dir, 'Data', 'geologic_unit_legend.txt')

        # Index counter for determining position in unit_names_list
        index = -1

        # Iterates through the list of unit names and capitalizes the first letter of each entry
        for name in self.unit_names_list:
            index += 1
            self.unit_names_list[index] = name.capitalize()

        # Lists of the unit names and colors to be included in the legend
        selected_unit_names = []
        selected_colors = []

        # Iterates through the dictionary of unit names and colors, capitalizes the first letter of each unit name, and then matches it with the list of inital unit names.
        # Then those unit names and colors are added to respective lists
        for name, color in self.cpt_data_dictionary.items():
            cap_name = name.capitalize()
            if cap_name in self.unit_names_list:
                selected_unit_names.append(cap_name)
                selected_colors.append(color)

        # Creates a postscript file and writes some explainer text and the column format
        with open(geo_legend, 'w') as f:
            f.write(
                '# G is vertical gap, V is vertical line, N sets # of columns,\n'
                '# D draws horizontal line, H is header, L is column header,\n'
                '# S is symbol,\n' 
                '# format of: symbol position, symbol type,\n' 
                '# format of: symbol size, symbol color, symbol border thickness, text position, text\n'

                'N 2\n'
            )

        # Iterates through the unit names and colors, and adds the symbol+text lines to the existing postscript file
        with open(geo_legend, 'a') as f:
            for color, name in zip(selected_colors, selected_unit_names):
                f.write(
                    'S 0.1i r 0.1i {} 0.1p 0.20i {}\n'
                    '\n'
                    .format(color, name)
                )



    # Plots the map    
    def Plot_Map(self):
        
        # Map save name
        save_name = os.path.join(self.main_dir, 'Results', 'Oregon_Geologic_Map_Demo.png')

        # Geologic unit polygons
        geo_unit_data = os.path.join(self.main_dir, 'Data', 'Conditioned_SHP', 'OR_geology_polygons_CONDITIONED.shp')

        # Geologic unit color palette
        geo_unit_color = os.path.join(self.main_dir, 'Data', 'geology_color_palette.cpt')

        geo_unit_legend = os.path.join(self.main_dir, 'Data', 'geologic_unit_legend.txt')

        # Extent defining the area of interest (Oregon) <min lon><max lon><min<lat><max lat>
        region = [-126.418246, -116.462397, 41.984295, 46.297196]

        # Map projection (Mercator): <type><size><units>
        projection = 'M6i' 

        # Frame  annotations: [<frame sides with/without ticks>, <x-axis tick rate>, <y-axis tick rate>]
        frame = ['SWne', 'xa', 'ya'] 

        # Polygon outline pens: <size><color>
        pens = {'geology':'0.1p,black'} 

        # Transparency of layer, transparency of save file background
        transparency = {'geology':50, 'save_file':False}    

        df_geo_polygons = gpd.read_file(geo_unit_data, driver = 'SHP')

        # Establishes figure to hold map layers
        fig = pygmt.Figure()

        # Forces ticks to display as degree decimal
        pygmt.config(FORMAT_GEO_MAP = 'D')

        # Forces the map frame annotation to be smaller
        pygmt.config(FONT_ANNOT_PRIMARY = '8p,Helvetica,black')


        #  Basemap layer
        fig.basemap(
            region = region,
            projection = projection,
            frame = frame
            )

        # Geologic unit layer
        fig.plot(
            # .gmt file - automatically detects polygon coordinates if in last column
            data = df_geo_polygons,
            # Sets polygon outline colour  
            pen = pens['geology'],
            # Sets polygon color map
            cmap = geo_unit_color,
            # Sets color to vary with selected column
            color = '+z',
            # Force close polygons
            close = True,
            # Sets the column used to map polygon colors (in this case colors polygons by name of geologic unit). Cloumn name appears to be lowercase as a product of conditioning
            aspatial = 'Z=ROCKTYPE1',
            # Sets layer transperancy
            transparency = transparency['geology'],
            # Commandline feedback for debugging 
            #verbose=True,  
            )

        # Plots the coastlines and political boundaries
        fig.coast(
            # Displays national boundaries (1) with 0.8 point gray40 lines, and does the same for state boundaries (2)
            borders = ['1/0.8p,gray40', '2/0.8p,gray40'], 
            # Displays coast outlines in 0.3 point black lines, and lakeshore outlines in .1 point black lines
            shorelines = ['1/0.3p,black', "2/0.1p,black"],
            # Sets resolution full (f) [highest setting]    
            resolution = 'f',
            # Sets water color
            water = 'lightskyblue2',  
            )

        # Plots a legend of the geologic unit names and respective colors
        fig.legend(
            spec = geo_unit_legend, # pslegend file
            position = 'jBL+o15.5/-4c+w10/12c', # plots text justifed bottom left (jBL) and offsets (+o) it by 15.5cm on the x-axis and -4cm on the y-axis (15.5/-4c), and establises width of columns(?)/legend area(?) (+w) as 10cm on the x-axis and 12cm on the y-axis (10/12c)
        )

        # Saves a copy of the generated figure
        fig.savefig(save_name, transparent = transparency['save_file'])



data = Map_Maker()

function_controls = [create_folders, condition_shp, create_cpt, create_legend, plot_map]
functions = [data.Create_Folders, data.Condition_Shapefile, data.Create_Color_Palette_Table, data.Create_Legend, data.Plot_Map]

for control, function in zip(function_controls, functions):
    if control == True:
        function()