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Add wavelength means Observation to analyze_spectral function #964

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Merged
nfahlgren merged 7 commits into from
Oct 11, 2022
Merged

Add wavelength means Observation to analyze_spectral function #964

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d8d8512
update var name and replace duplicate observation
HaleySchuhl Oct 4, 2022
3462534
missed one var name update
HaleySchuhl Oct 5, 2022
7a6a0e6
update doc page to reflect measurements getting recorded
HaleySchuhl Oct 11, 2022
91f7b1a
relabel scale of new obs
HaleySchuhl Oct 11, 2022
d98f09a
change dtype to list
HaleySchuhl Oct 11, 2022
276a04d
fix duplicate
HaleySchuhl Oct 11, 2022
5691e90
ugh rename in testing too
HaleySchuhl Oct 11, 2022
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3 changes: 2 additions & 1 deletion docs/analyze_spectral.md
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Expand Up @@ -14,7 +14,8 @@ the values out as observations to get saved out. Can also print out a histogram
- label - Optional label parameter, modifies the variable name of observations recorded. (default `label="default"`)
- **Example use:**
- Below
- **Output data stored:** Data ('max_reflectance', 'min_reflectance', 'median_reflectance', 'spectral_std', 'spectral_frequencies', 'global_mean_reflectance', 'global_median_reflectance', 'global_spectral_std') automatically gets stored to the
- **Output data stored:** Data ('global_mean_reflectance', 'global_median_reflectance', 'global_spectral_std', 'wavelength_means', 'max_reflectance',
'min_reflectance', 'spectral_std', 'spectral_frequencies') automatically gets stored to the
[`Outputs` class](outputs.md) when this function is ran.
These data can always get accessed during a workflow (example below). For more detail about data output see [Summary of Output Observations](output_measurements.md#summary-of-output-observations)

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12 changes: 6 additions & 6 deletions plantcv/plantcv/hyperspectral/analyze_spectral.py
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Expand Up @@ -39,7 +39,7 @@ def analyze_spectral(array, mask, histplot=None, label="default"):
wavelength_data = array_data[np.where(mask > 0)]

# Calculate mean reflectance across wavelengths
wavelength_freq = wavelength_data.mean(axis=0)
wavelength_means = wavelength_data.mean(axis=0)
max_per_band = wavelength_data.max(axis=0)
min_per_band = wavelength_data.min(axis=0)
std_per_band = wavelength_data.std(axis=0)
Expand All @@ -58,7 +58,7 @@ def analyze_spectral(array, mask, histplot=None, label="default"):

for i, wavelength in enumerate(array.wavelength_dict):
new_wavelengths.append(wavelength)
new_freq.append((wavelength_freq[i]).astype(float))
new_freq.append((wavelength_means[i]).astype(float))
new_std_per_band.append(std_per_band[i].astype(float))
new_max_per_band.append(max_per_band[i].astype(float))
new_min_per_band.append(min_per_band[i].astype(float))
Expand All @@ -83,9 +83,9 @@ def analyze_spectral(array, mask, histplot=None, label="default"):
trait='pixel-wise standard deviation per band',
method='plantcv.plantcv.hyperspectral.analyze_spectral', scale='None', datatype=float,
value=float(std_reflectance), label='reflectance')
outputs.add_observation(sample=label, variable='global_spectral_std', trait='pixel-wise standard deviation ',
method='plantcv.plantcv.hyperspectral.analyze_spectral', scale='None', datatype=float,
value=float(std_reflectance), label='reflectance')
outputs.add_observation(sample=label, variable='wavelength_means', trait='pixel-wise standard deviation ',
method='plantcv.plantcv.hyperspectral.analyze_spectral', scale='reflectance', datatype=list,
value=wavelength_means, label=wavelength_labels)
outputs.add_observation(sample=label, variable='max_reflectance', trait='maximum reflectance per band',
method='plantcv.plantcv.hyperspectral.analyze_spectral', scale='reflectance', datatype=list,
value=new_max_per_band, label=wavelength_labels)
Expand All @@ -100,7 +100,7 @@ def analyze_spectral(array, mask, histplot=None, label="default"):
value=new_freq, label=wavelength_labels)

dataset = pd.DataFrame({'Wavelength (' + array.wavelength_units + ')': new_wavelengths,
'Reflectance': wavelength_freq})
'Reflectance': wavelength_means})
mean_spectra = (ggplot(data=dataset,
mapping=aes(x='Wavelength (' + array.wavelength_units + ')', y='Reflectance'))
+ geom_line(color='purple')
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