refactor project and add fluorescence data

Author: paucablop

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

Pipfile

@@ -22,6 +22,7 @@ six = "==1.16.0"
 threadpoolctl = "==3.1.0"
 kineticmodels = "==0.0.10"
 packaging = "==21.3"
+pytest = "*"
 
 [dev-packages]
 ipykernel = "*"

Pipfile.lock

@@ -1 +0,0 @@
-from ._base import load_training_data, load_fermentation_spectra_data, load_fermentation_hplc_data

example.ipynb

@@ -0,0 +1 @@
+from ._base import load_filtered_fluorescence_data, load_unfiltered_fluorescence_data

fermentools/datasets/__init__.py

@@ -0,0 +1,37 @@
+import numpy as np
+import os
+
+PACKAGE_DIRECTORY = os.path.dirname(os.path.abspath(__file__))
+
+def load_filtered_fluorescence_data():
+    """
+    returns the emission - excitation matrix for the filtered data
+    @return fluorescence_spectra: tensor with the filtered data (sample x excitation x emission)
+    @return emission_wavelengths: array with the emission wavelengths
+    @return excitation_wavelengths: array with the excitation wavelengths
+    """
+
+    fluorescence_spectra = np.genfromtxt(PACKAGE_DIRECTORY + "/data/excitation_emission_matrix.csv", delimiter=",")
+    emission_wavenumbers = np.genfromtxt(PACKAGE_DIRECTORY + "/data/emission_wavenumbers.csv", delimiter=",")
+    excitation_wavenumbers = np.genfromtxt(PACKAGE_DIRECTORY + "/data/excitation_wavenumbers.csv", delimiter=",")
+
+    fluorescence_spectra = fluorescence_spectra.reshape(20, 43, 91)
+
+    return fluorescence_spectra[0:10,:,:], emission_wavenumbers, excitation_wavenumbers
+
+
+def load_unfiltered_fluorescence_data():
+    """
+    returns the emission - excitation matrix for the filtered data
+    @return fluorescence_spectra: tensor with the unfiltered data (sample x excitation x emission)
+    @return emission_wavelengths: array with the emission wavelengths
+    @return excitation_wavelengths: array with the excitation wavelengths
+    """
+    
+    fluorescence_spectra = np.genfromtxt(PACKAGE_DIRECTORY + "/data/excitation_emission_matrix.csv", delimiter=",")
+    emission_wavenumbers = np.genfromtxt(PACKAGE_DIRECTORY + "/data/emission_wavenumbers.csv", delimiter=",")
+    excitation_wavenumbers = np.genfromtxt(PACKAGE_DIRECTORY + "/data/excitation_wavenumbers.csv", delimiter=",")
+
+    fluorescence_spectra = fluorescence_spectra.reshape(20, 43, 91)
+
+    return fluorescence_spectra[10:20,:,:], emission_wavenumbers, excitation_wavenumbers

fermentools/datasets/fluorescence/__init__.py

@@ -0,0 +1,73 @@
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+6.000000000000000000e+02

fermentools/datasets/fluorescence/_base.py

@@ -0,0 +1,43 @@
+2.400000000000000000e+02
+2.450000000000000000e+02
+2.500000000000000000e+02
+2.550000000000000000e+02
+2.600000000000000000e+02
+2.650000000000000000e+02
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fermentools/datasets/data/__init__.py renamed to fermentools/datasets/fluorescence/data/__init__.py

@@ -0,0 +1 @@
+from ._base import load_training_data, load_fermentation_spectra_data, load_fermentation_hplc_data

fermentools/datasets/fluorescence/data/emission_wavenumbers.csv

@@ -1,6 +1,7 @@
-from dtuprosys.datasets import load_training_data, load_fermentation_spectra_data, load_fermentation_hplc_data
+from fermentools.datasets.ir import load_training_data, load_fermentation_spectra_data, load_fermentation_hplc_data
+from fermentools.datasets.fluorescence import load_filtered_fluorescence_data, load_unfiltered_fluorescence_data
 
-def test_train_loadings():
+def test_ir_train_loadings():
   """
   Test the loading of the training data.
   """
@@ -14,7 +15,7 @@ def test_train_loadings():
   assert reference.shape == (21, 1)
 
 
-def test_fermentation_loadings():
+def test_ir_fermentation_loadings():
   """
   Test the loading of the fermentation data.
   """
@@ -27,3 +28,18 @@ def test_fermentation_loadings():
   # Assert
   assert spectra.shape == (1629, 1047)
   assert reference.shape == (34, 6)
+
+
+def test_fluorescence_loadings():
+  """
+  Test the loading of the fluorescence data
+  """
+  # Arrange
+
+  # Act
+  eem_filtered, excitation_wavenumbers, emission_wavenumbers = load_filtered_fluorescence_data()
+  eem_unfiltered, _, _ = load_unfiltered_fluorescence_data()
+
+  # Assert
+  assert eem_filtered.shape == (10, 43, 91)
+  assert eem_unfiltered.shape == (10, 43, 91)

fermentools/datasets/fluorescence/data/excitation_emission_matrix.csv

@@ -1,5 +1,5 @@
-from dtuprosys.datasets import load_training_data
-from dtuprosys.chemometrics.preprocessing import RangeCut, Derivative
+from fermentools.datasets.ir import load_training_data
+from fermentools.chemometrics.preprocessing import RangeCut, Derivative
 
 import pandas as pd