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creating function main #4

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creating function main #4

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36fce4d
Initial commit creating main
aajayi-21 Jun 21, 2023
2ffed0c
Merge branch 'main' of github.com:diffpy/diffpy.snmf into create_main
aajayi-21 Jul 17, 2023
42dac41
reformatted
aajayi-21 Jul 17, 2023
dfa4910
setup library behavior
aajayi-21 Jul 18, 2023
b982382
updated main, fixed io
aajayi-21 Jul 18, 2023
6d8be90
added create_parser function to handle application input
aajayi-21 Jul 19, 2023
6fb2879
added the maximum iterations variable and the condition for when the …
aajayi-21 Jul 19, 2023
07cd3ec
renamed parameters and added output directory parameter. Added functi…
aajayi-21 Jul 20, 2023
1be46c2
Merge branch 'main' into create_main
aajayi-21 Jul 20, 2023
32bf269
added import statement, synced main with branch
aajayi-21 Jul 20, 2023
e527a19
added functionality to test cli app
aajayi-21 Jul 21, 2023
865251e
added explicit default value for --input-directory and modified help …
aajayi-21 Jul 21, 2023
8f6b94e
changed import statement to explicitly import functions
aajayi-21 Jul 21, 2023
a174475
reformatted io.py, moved version argument to bottom of create_parser,…
aajayi-21 Jul 22, 2023
8b26f4f
changed "component_amount" to "number_of_components" in io.py. change…
aajayi-21 Jul 22, 2023
a024bb5
fixed typo out-directory help string
aajayi-21 Jul 22, 2023
1331805
changed 'xrd' to 'power_diffraction' choices for data_type, renamed v…
aajayi-21 Jul 24, 2023
7d4c97f
added a lifting factor optional argument
aajayi-21 Jul 26, 2023
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6 changes: 4 additions & 2 deletions diffpy/snmf/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,14 +44,16 @@ def initialize_variables(data_input, component_amount, data_type, sparsity=1, sm

component_matrix_guess = np.random.rand(signal_length, component_amount)
weight_matrix_guess = np.random.rand(component_amount, moment_amount)
stretching_matrix_guess = np.ones(component_amount, moment_amount) + np.random.randn(component_amount,
stretching_matrix_guess = np.ones((component_amount, moment_amount)) + np.random.randn(component_amount,
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these should probably not be in io.py. I would suggest to make functions somewhere in subroutines that initialize specific arrays then here write something like:

stretching_matrix_guess = initialize_arrays(number_of_components, number_of_moments)

or sthg like that.

In the function in subroutines.py, put into docstring what the arrays are and how the decision were made on how to do it. Currently the code is a bit too hard to read as it is....I think that by component_amount , based on earlier conversations, you mean number_of_components. I have no idea what moment_amount means, nor why you initialize it with ones and then add some kind of random component, so a docstring could be veyr helpful here (but in subroutines, not in io.

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I will create that function on a new branch. I will also rename the variables to make it more clear.

moment_amount) * 1e-3

diagonals = [np.ones(moment_amount - 2), -2 * np.ones(moment_amount - 2), np.ones(moment_amount - 2)]
smoothness_term = .25 * scipy.sparse.diags(diagonals, [0, 1, 2], shape=(moment_amount - 2, moment_amount))

hessian_helper_matrix = scipy.sparse.block_diag([smoothness_term.T @ smoothness_term] * component_amount)
sequence = np.arange(moment_amount * component_amount).reshape(component_amount, moment_amount).T.flatten()

hessian_helper_matrix = hessian_helper_matrix.tocsr()
hessian_helper_matrix = hessian_helper_matrix[sequence, :][:, sequence]

return {
Expand Down Expand Up @@ -102,7 +104,7 @@ def load_input_signals(file_path=None):
for item in directory_path.iterdir():
if item.is_file():
data = loadData(item.resolve())
if current_grid and current_grid != data[:, 0]:
if len(current_grid) != 0 and (current_grid != data[:, 0]).any():
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I think a comment line would help here with the intent. I.e., why do we ignore and not handle if the data are on a different grid. If I remember correctly t here was a physics reason (mathematically it should be straightforward). Just recording for future people.

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I will add a comment line to explain this

print(f"{item.name} was ignored as it is not on a compatible grid.")
continue
else:
Expand Down
23 changes: 22 additions & 1 deletion diffpy/snmf/stretchednmfapp.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,26 @@
import numpy as np

from diffpy.snmf.io import load_input_signals, initialize_variables


def main():
print("Hello World!")
directory_path = input("Specify Path (Optional. Press enter to skip):")
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if not directory_path:
directory_path = None

data_type = input("Specify the data type ('xrd' or 'pdf'): ")
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this can often be obtained from file header.

if data_type != 'xrd' and data_type != 'pdf':
raise ValueError("The data type must be 'xrd' or 'pdf'")

component_amount = input("\nEnter the amount of components to obtain:")
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should probably be "number" of components. "amount" sounds like a quantity of a continuous quantity, like amount of sand or amount of flour.

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I will change the naming.

try:
component_amount = int(component_amount)
except TypeError:
raise TypeError("Please enter an integer greater than 0")
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put this in the input instructions rather than have the poor user have to enter quantities and have the program fail to find out they were supposed to put in an integer...

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Ok. I will do this


grid, data_input = load_input_signals(directory_path)
variables = initialize_variables(data_input, component_amount, data_type)
lifted_data = data_input - np.ndarray.min(data_input[:])


if __name__ == "__main__":
Expand Down