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docs: some parts in documentation are incorrect. #352
Description
Problems
- Failed example for DiffractionObject.get_array_index
- Duplicate code block
- Failed example for diffpy.utils.transform.d_to_tth
- Markup not rendered correctlly
failed example for DiffractionObject.get_array_index
In Diffraction Objects Example documentation step 4
tth_ninety_index = diff_object1.get_array_index(90, xtype="tth")
will raise
TypeError: DiffractionObject.get_array_index() got multiple values for argument 'xtype'
Because the signature is
def get_array_index(self, xtype, value):
...
failed example for diffpy.utils.transform.d_to_tth
In https://www.diffpy.org/diffpy.utils/examples/transforms_example.html#id1, step 3
from diffpy.utils.transforms import d_to_tth wavelength = 0.71 d = np.array([1.0, 0.8, 0.6, 0.4, 0.2]) tth = d_to_tth(d, wavelength)
will raise
ValueError: The supplied input array and wavelength will result in an impossible two-theta. Please check these values and re-instantiate the DiffractionObject with correct values.
duplicate code block
In https://www.diffpy.org/diffpy.utils/examples/resample_example.html#resampling-example, step 1. The same code block and words appear twice. This might be a typo.
markup not rendered correctly
In https://www.diffpy.org/diffpy.utils/examples/parsers_example.html#id1, step 5. A sentence is included in a code block.
Activity
ycexiao commented on Jul 24, 2025
The function DiffractionObject.get_array_index
def get_array_index(self, xtype, xvalue): """Return the index of the closest value in the array associated with the specified xtype and the value provided. ... xtype = self._input_xtype xarray = self.on_xtype(xtype)[0] if len(xarray) == 0: raise ValueError( f"The '{xtype}' array is empty. " "Please ensure it is initialized." ) index = (np.abs(xarray - xvalue)).argmin() return index """So the input parameterxtype doesn't have an effect at all. Thus, the following code
x = np.linspace(0, 90, 1000) y = np.random.rand(1000) tmp = DiffractionObject( xarray=x, yarray=y, xtype="angle", wavelength=1.54, ) index_angle = tmp.get_array_index(xvalue=0.24, xtype="angle") index_q_from_function = tmp.get_array_index(xvalue=0.24, xtype="q") real_index_q = np.argmin(np.abs(tmp.on_xtype("q")[0] - 0.24)) print(index_angle == index_q_from_function) print(index_q_from_function == real_index_q)returns True and False.
@sbillinge, is it a bug we want to fix?
sbillinge commented on Jul 25, 2025
yes, this looks like a bug. The intent is that the user wants the index of, for example, Q=23.4 a-1, or tth=45 deg. so inside we want to use the relevant xarray, be it Q or tth or whatever.
Let's write some tests for this then fix the code.
Please check everywhere in the code where this is used, and also the docs so everything agrees. Maybe do all that work on separate PR clsing a separate issue.
Please also fix all the other documentation issues that you found.