sedimentanalyst

Sediment Analyst is a modularized Python package and dash app that enables sedimentological analyses. By using sieving datasets as input, Sediment Analyst computes sediment statistics. For a complete list of computed statistics see section below (Outputs). For using our app, please watch our video tutorial here.

Important

Checkout the package requirements file in the Github repository for installing the necessary processing libraries.

Outputs and Capabilities

Sediment Analyst computes the following:

  • A summary of sediment characteristics, which can be exported as csv:
  • Cumulative grain size distribution curves, which are available as:

    • Static plots per sample with the analyzer subpackage.

    • Interactive plots with user-selected samples using the app subpackage.

sedimentanalyst

sedimentanalyst package

Subpackages
sedimentanalyst.analyzer package
Submodules
sedimentanalyst.analyzer.config module

This module contains all the imported packages (dependencies) and user inputs for running the classes StatisticalAnalyzer and StaticPlotter.

sedimentanalyst.analyzer.config.get_input()
sedimentanalyst.analyzer.main module

Main script to exemplify the use of Sediment Analyst

Authors: Beatriz Negreiros and Federica Scolari

sedimentanalyst.analyzer.main.main()
sedimentanalyst.analyzer.static_plotter module

Module designated for the class StaticPlotter

Author : Federica Scolari

class sedimentanalyst.analyzer.static_plotter.StaticPlotter(analyzer)

Bases: object

A class for creating the static plots of the cumulative grain size distribution curves

analyzer

StatisticalAnalyzer object containing all the computed sample statistics. For more information check the Class StatisticalAnalyzer

Type

StatisticalAnalyzer

cum_df

DataFrame containing the Grain Sizes [mm] and the corresponding Cumulative Percentage [%]

cum_plotter(output)

Plots the cumulative grain size distribution curve for each sample

cum_plotter(output)

Method to output the cumulative grain size distribution curve and save it as an image.

Parameters

output (str) – Name of the image containing the outputs

Returns

None

sedimentanalyst.analyzer.statistical_analyzer module

Module designated for class StatisticalAnalyzer

Author : Beatriz Negreiros

class sedimentanalyst.analyzer.statistical_analyzer.StatisticalAnalyzer(sieving_df=None, metadata=None)

Bases: object

A class for computing statistical sedimentological parameters using sieving datasets (class weights and grain size).

original_df

dataframe containing in the first column the grain sizes diameters (in mm) and in the second column the fraction mass that passes through the corresponding diameter.

Type

df

cumulative_df

dataframe containing in the first column the grain sizes diameters (in mm) and in the second column the cumulative percentages (% in mass, in grams) that passes through the corresponding grain size diameters.

Type

df

statistics_df

dataframe containing all the statistics of the sample, which includes: d10, d16, d25, d30, d50, d60, d75, d84, d90, Mean Grain Site dm [mm], Geometrical mean grain size dg [mm], Sorting Index, Fredle Index, Grain Size standard deviation, skewness, kurtosis, coefficient of uniformity Cu, curvature coefficient Cc.

Type

df

porosity_conductivity_df

dataframe containing the porosity estimators (estimated from the grain size analysis) according to different literature, as well as the corresponding hydraulic conductivity estimator for each of the porosity values according to the Kozeny Carman Equation.

Type

df

samplename

sample name

Type

str

coords

x and y coordinates, in this order

Type

tuple

porosity

porosity values set up by the user, possibly via alternative measurements, such as with photogramic approaches.

Type

float

sf_porosity

sphericity index. For rounded sediments it equals 6.10

Type

float

compute_cumulative_df(df)

computes cumulative_df dataframe

compute_statistics_df(df)

computes statistics_df dataframe

compute_porosity_conductivity_df(df)

computes porosity_conductivity_df dataframe

Note

See more on the determination of riverbed porosity from Freezecore samples via a Structure from Motion approach at Seitz 2020.

compute_cumulative_df()

Compute two new columns in the grain size dataframe, which are + Percentage Fraction [%] and + Cumulative Percentage [%]

compute_porosity_conductivity_df()

Compute porosity predictors and corresponding hydraulic conductivities (for each estimated porosity value)

compute_statistics_df()

Fills a dataframe (self.statistics_df) with all relevant statistics by calling smaller private methods

print_excel(file_name='statistics.xlsx')

Print all attribute dataframes into excel sheet output is saved into local folder “outputs”

Parameters

file_name (str) – Path to save the file

sedimentanalyst.analyzer.utils module

Module containing auxiliary functions to handle the StatisticalAnalyzer class and for running main.py

Author: Beatriz Negreiros and Federica Scolari

sedimentanalyst.analyzer.utils.append_global(obj=None, df=None)

A function to append all information stemming from the class Statistical Analyzer into one dataframe for further filtering and analyses

Parameters
Returns

appended dataframe with statistics of sample file

Return type

df

sedimentanalyst.analyzer.utils.extract_df(dic=<built-in function input>, file=None)

Function to extract parsed datafiles and tabularize it into dataframe.

Parameters

  • dic (dict) – global input parameters that can be altered in the config.py file

  • file (str) – path name of the file containing a sieving sample

Returns

dataframe containing grain sizes and class weights (parsed according to the config.py) list: list of sample’s information as following: [samplename, sampledate, (lat, long), porosity,

sf_porosity], parsed accoridng to the config.py.

Return type

df

sedimentanalyst.analyzer.utils.find_files(folder=None)

Lists the files in the folder indicated

Parameters

folder (str) – path of the folder to scan (to look for .xlxs files)

Returns

list of strings from addresses of all files inside the folder

Return type

list

Module contents
sedimentanalyst.app package
Submodules
sedimentanalyst.app.accessories module

Accessory elements for the web app

Author: Beatriz Negreiros

class sedimentanalyst.app.accessories.Accessories

Bases: object

A class for allocating accessories elements for the Dash app, including layout and Dash component settings, extensive callouts and parsing of input contents.

style_upload

style information for a dropbox component

Type

dict

intro_text

markdown test for introducing the app

Type

dash.dcc.Markdown.Markdown

inputs_text

markdown text for explaining the inputs

Type

dash.dcc.Markdown.Markdown

img_style

style information for formatting images

Type

dict

input_boxes

list of Input objects for enabling user to enter the indexing information to read from user’s files

Type

list

style_graph
Type

dict

style_statistic

style information for the statistic dropdown

Type

dict

parse_contents(tuple)

tuple of object (sedimentanalyst.analyzer.StatisticalAnalyzer) plus an object of

type html.Div with reading messages.
parse_contents(contents, filename, date, input_dict_app)
Parameters

  • contents (dash.dcc.Input.Input) – Contents of the file containing the sample data (class weights and

  • sizes) (corresponding grain) –

  • filename (dash.dcc.State.State) – Filename

  • date (dash.dcc.State.State) – date of last modified

  • input_dict_app (dict) – Index parameters input by the user necessary to read and parse the contents of the file

Returns

object for accessing necessary attributes of the class.

Return type

StatisticalAnalyzer

sedimentanalyst.app.appconfig module
sedimentanalyst.app.interac_plotter module

Module designated for the class InteractivePlotter

Author : Federica Scolari

class sedimentanalyst.app.interac_plotter.InteractivePlotter(df)

Bases: object

A class for creating interactive plots for the comparison of the statistical analysis results

df

DataFrame containing the information from the statistical analysis

Type

pandas.core.frame.DataFrame

convert_coordinates(df, projection)

Transforms the coordinates of a given projection to degrees

create_map(df, projection, samples=None)

Creates a scatter map

plot_barchart(param, samples)

Plots the user-selected parameter for all samples in a bar chart

plot_gsd(samples)

Plots the cumulative grain size distribution curve for all samples using a line chart

plot_diameters(samples)

Plots the calculated sediment diameters in a bar chart for all samples

convert_coordinates(df, projection)

Method which transforms the coordinates of a give projection to degrees.

Parameters

  • df (pandas.core.frame.DataFrame) – DataFrame on which the coordinate transformation is applied

  • projection (str) – Name of the initial projection

Returns

DataFrame object on which the coordinate transformation has been applied

Return type

pandas.core.frame.DataFrame

create_map(df, projection='epsg:3857', samples=None)

Creates a scatter map based on the DataFrame.

Parameters

  • df (DataFrame) – DataFrame on which the coordinate transformation has been applied

  • projection (str) – Name of the initial projection

  • samples (list) – Names of the collected samples

Returns

Figure object that allows the visualization of the Open Street map of the area where the samples were collected

Return type

plotly.graph_objects.Figure

plot_barchart(param, samples)

Method that outputs the results in a bar chart for the interactive comparison of the results.

Parameters

  • param (str) – Statistical parameters selectable from the user

  • samples (list) – Names of the collected samples

Returns

Figure object that allows the visualization of the plot of a

bar chart in which the statistical parameter selected by the user is shown for each selected sample

Return type

plotly.graph_objects.Figure

plot_diameters(samples)

Method which plots the calculated sediment diameters in a bar chart for all selected samples.

Parameters

samples (list) – Names of the collected samples

Returns

Figure object allowing to visualize the calculated diameters (d10, d16, d25, d30, d50, d60, d75, d84 and d90) for all the collected samples

Return type

plotly.graph_objects.Figure

plot_gsd(samples)

Method which plots the cumulative grain size distribution curve for all selected samples.

Parameters

samples (list) – Names of the collected samples

Returns

Figure object enabling the visualization of the plot of the grain

size distribution curve for all collected sample by using a line chart

Return type

plotly.graph_objects.Figure

sedimentanalyst.app.web_application module

Stand-alone designated for the web application

Author : Beatriz Negreiros

sedimentanalyst.app.web_application.download_summary_stats(data, n_clicks)
sedimentanalyst.app.web_application.parse_and_analyse(list_of_contents, list_of_names, list_of_dates, input_dict_in_layout, click)
sedimentanalyst.app.web_application.save_inputs(header, gs_clm, cw_clm, n_rows, porosity, sf_porosity, index_lat, index_lon, sample_name_index, sample_date_index, projection, n_clicks)
sedimentanalyst.app.web_application.update_barchart(data, stat_value, samples)
sedimentanalyst.app.web_application.update_diameters(data, samples)
sedimentanalyst.app.web_application.update_gsd(data, samples)
sedimentanalyst.app.web_application.update_map(data, dict_to_get_proj, samples)
sedimentanalyst.app.web_application.update_sample_id(n_clicks, data)
sedimentanalyst.app.web_application.update_stat_drop(n_clicks, data)
Module contents
Module contents

Indices and tables