Refactor - use functions to generate outputs in `main`

[bobleesj]

Problem

In main, 4 figures and .json/.csv are generated below:

 fig1 = nmf.component_plot(df_components, args1.xrd, args1.x_units, args1.show)
 fig2 = nmf.component_ratio_plot(df_component_weight_timeseries, args1.show)
 fig3 = nmf.reconstruction_error_plot(df_reconstruction_error, args1.show)
 if args1.pca_thresh:
 fig4 = nmf.explained_variance_plot(df_explained_var_ratio, args1.show)

 if args1.save_files:
 if not os.path.exists(os.path.join(os.getcwd(), "nmf_result")):
 os.mkdir(os.path.join(os.getcwd(), "nmf_result"))
 output_fn = datetime.fromtimestamp(time.time()).strftime("%Y%m%d%H%M%S%f")
 df_components.to_json(os.path.join(os.getcwd(), "nmf_result", "x_index_vs_y_col_components.json"))
 df_component_weight_timeseries.to_json(
 os.path.join(os.getcwd(), "nmf_result", "component_index_vs_pratio_col.json")
 )
 df_component_weight_timeseries.to_csv(
 os.path.join(os.getcwd(), "nmf_result", output_fn + "component_row_pratio_col.txt"),
 header=None,
 index=False,
 sep=" ",
 mode="a",
 )
 df_reconstruction_error.to_json(
 os.path.join(os.getcwd(), "nmf_result", "component_index_vs_RE_value.json")
 )
 plot_file1 = os.path.join(os.getcwd(), "nmf_result", output_fn + "comp_plot.png")
 plot_file2 = os.path.join(os.getcwd(), "nmf_result", output_fn + "ratio_plot.png")
 plot_file3 = os.path.join(os.getcwd(), "nmf_result", output_fn + "loss_plot.png")
 if args1.pca_thresh:
 plot_file7 = os.path.join(os.getcwd(), "nmf_result", output_fn + "pca_var_plot.png")
 plot_file4 = os.path.splitext(plot_file1)[0] + ".pdf"
 plot_file5 = os.path.splitext(plot_file2)[0] + ".pdf"
 plot_file6 = os.path.splitext(plot_file3)[0] + ".pdf"
 if args1.pca_thresh:
 plot_file8 = os.path.splitext(plot_file7)[0] + ".pdf"
 txt_file = os.path.join(os.getcwd(), "nmf_result", output_fn + "_meta" + ".txt")
 with open(txt_file, "w+") as fi:
 fi.write("NMF Analysis\n\n")
 fi.write(f"{len(df_component_weight_timeseries.columns)} files uploaded for analysis.\n\n")
 fi.write(f"The selected active r ranges are: {args1.xrange} \n\n")
 fi.write("Thesholding:\n")
 fi.write(f"\tThe input component threshold was: {args1.threshold}\n")
 fi.write(f"\tThe input improvement threshold was: {args1.improve_thresh}\n")
 fi.write(f"\tThe input # of iterations to run was: {args1.n_iter}\n")
 fi.write(f"\tWas PCA thresholding used?: {args1.pca_thresh}\n")
 fi.write(f"{len(df_components.columns)} components were extracted")

 fig1.savefig(plot_file1)
 fig2.savefig(plot_file2)
 fig3.savefig(plot_file3)
 if args1.pca_thresh:
 fig4.savefig(plot_file7)
 fig1.savefig(plot_file4)
 fig2.savefig(plot_file5)
 fig3.savefig(plot_file6)

Solution

The code needs to be refactored - make variables name more explicit. Ex) plot_file1 - plot_file_4 which is a .pdf plot of plot_file1.

[sbillinge]

also, break it out into functions that are called by main.