import nmf_mapping_code as nmf

README.rst

@@ -105,70 +105,6 @@ and run the following ::
 Getting Started
 ---------------
 
-Input:
-- directory: path to the directory containing the diffraction files that are to be analyzed
-    - format: string (filepath)
-        - eg: '/Users/zthatcher/Desktop/Data/nmf_mapping/time_data/' or . for cwd
-
-- save-files (optional): boolean as to whether or not you would like to save the dataframes, plots, and
-components (note: pdf data saves as .cgr and xrd data saves as .xy)
-    - format: boolean
-        - eg: --save-files False
-    - default: True
-
-- threshold (optional and mut-exc to other thresholds): a threshold for the number of structural phases graphed (NMF components returned)
-    - format as: integer
-        - eg: --threshold 2
-    - default: 10
-
-- improve-thresh (optional and mut-exc to other thresholds): a threshold (between 0 and 1) for the relative improvement ratio necessary to
-  add an additional component. Default is 0.001. 0.1 Recommended for real data.
-    - format: float
-        - eg: --improve-thresh 0.1
-    - default = 0.001
-
-- pca-thresh (optional and mut-exc to other thresholds): explained variance threshold for PCA component counting cutoff
-    - format: float
-        - eg: --pca-thresh 0.95
-    - default = None
-
-- n-iter (optional): total number of iterations to run NMF algo. Defaults to 1000. 10000 typical to publish.
-    - format: int
-        - eg: --n-iter 10000
-    - default: 1000
-
-- x-range (optional): the active x-range over which to run the NMF analysis (must be between shortest and
-longest range in the set of files)
-    - format: pair of integers representing the lower r bound and the upper r bound with a comma between
-    the lower and upper bound
-        -  eg: --xrange 5,10 12,15
-    - default: entire range
-
-- xrd (optional): set this option if the directory contains xy or xye files rather than gr.
-    - format: boolean
-        - eg: --xrd True
-    - default: False
-
-- x_units (required if xrd): set this as either twotheta or q if working with xrd data.
-    - format: enum[str]
-        - eg: --x_units twotheta
-    - default: None (since --xrd defaults to False)
-
-- show graphs (optional): whether you or not you would like display the images
-    - format: boolean
-        - eg: --show False
-    - default: True
-
-Returns:
-- Figure One: PDF or XRD pattern of structural phase components contributing to the NMF reconstruction
-- Figure Two: Weights of the phase components plotted in Figure One
-- Figure Three: Reconstruction error as a function of components
-- (Optional) Figure Four: Explained Variance plot as a function of components for PCA thresholding
-
-Example:
-
-nmf_mapping . --threshold 3 --xrange 5,10 --show True
-
 
 You may consult our `online documentation <https://diffpy.github.io/diffpy.nmf_mapping>`_ for tutorials and API references.
 

src/diffpy/nmf_mapping/main.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from diffpy.nmf_mapping import nmf
+import diffpy.nmf_mapping.nmf_mapping_code as nmf
 
 
 def boolean_string(s):

src/diffpy/nmf_mapping/nmf_mapping_code.py

@@ -16,7 +16,7 @@
 from sklearn.decomposition import NMF, PCA
 from sklearn.exceptions import ConvergenceWarning
 
-plt.style.use(all_styles["bg_style"])
+plt.style.use(all_styles["bg-style"])
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=ConvergenceWarning)
 

tests/test_load_data.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from diffpy.nmf_mapping import nmf
+import diffpy.nmf_mapping.nmf_mapping_code as nmf
 
 dir = pathlib.Path(__file__).parent.resolve()