compute mu by yucongalicechen · Pull Request #278 · diffpy/diffpy.utils

yucongalicechen · 2024-12-26T16:48:34Z

closes#45
@sbillinge ready for review. I can add docs in the same PR once we're happy with the function

codecov · 2024-12-26T16:51:03Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (e72022e) to head (dd52ad9).
Report is 16 commits behind head on main.

Additional details and impacted files

@@ Coverage Diff @@## main #278 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 8 8 Lines 496 500 +4 =========================================
+ Hits 496 500 +4

Files with missing lines	Coverage Δ
tests/test_tools.py	`100.00% <100.00%> (ø)`

sbillinge

please see inline

sbillinge · 2024-12-26T17:04:48Z

+
+ Parameters
+ ----------
+ sample str


I think we would normally do tihs as:
sample: str The chemical formula or the name of the material
i.e., colon and sentencecse

sbillinge · 2024-12-26T17:05:24Z

+ the chemical formula or the name of the material
+ energy float
+ the energy in eV
+ density float or None


density: float, optional, Default is None

sbillinge · 2024-12-26T17:06:47Z

+ energy float
+ the energy in eV
+ density float or None
+ material density in gr/cm^3


this should be "sample mass density" or even better, "mass density of the packed powder/sample" to be clear. the material desnsity is something quite different (mass of atoms in the unit cell divided by unit cell volume)

sbillinge · 2024-12-26T17:07:50Z

 return metadata
+
+
+def compute_mu_using_xraydb(sample, energy, density=None):


let's change sample to composition or maybe sample_composition.
I think we probably need packing_fraction as an optional arg.

sbillinge · 2024-12-26T17:30:37Z

 assert actual_metadata == expected
+
+
+def test_compute_mu_using_xraydb():


we need a test for no density passed in. Also for packing fraction passed in and also for both passed in. Think about what behavior you want in each of these cases and write a "case" (look elsewhere in test_tools for how we are handling this now)

yucongalicechen · 2024-12-26T20:01:09Z

@sbillinge ready for another review

yucongalicechen · 2024-12-26T20:02:35Z

 return metadata
+
+
+def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):


added packing fraction. does this make sense or should we use None instead? I think if we set the default to 1 the code can be more concise

I think setting to None is clearer here. The logic from the perspective of the user is that we either have a packing fraction or we don't. If it is None, you can set it to 1 in the code.

Also, didn't we discuss to change the name to sample_mass_density?

yucongalicechen · 2024-12-26T20:03:36Z

+ ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 1}, 0.5330),
+ ({"sample_composition": "H2O", "energy": 10000, "density": 0.4985, "packing_fraction": 1}, 0.2665),
+ # C4: user specified a standard density and a packing fraction
+ ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 0.5}, 0.2665),


added test cases with description. I didn't include the bad cases where the user does not specify a density and xraydb doesn't know the density (this is taken care by xraydb)

bobleesj · 2024-12-26T20:05:46Z

- sample, energy, density = "ZrO2", 17445.362740959618, 1.009
- actual_mu = compute_mu_using_xraydb(sample, energy, density=density)
- assert actual_mu == pytest.approx(1.252, rel=1e-4, abs=0.1)
+params_mu = [


Could you please follow the guides provided here? https://gitlab.thebillingegroup.com/resources/group-wiki/-/wikis/Group-standards-for-pytest-and-docstrings
add higher level function purpose, use descriptive yet concise variable names, no need to create extra variable of params_mu, no need to add "user specific, etc."

@yucongalicechen
@sbillinge if you have also further suggestions to the gitlab doc, please suggest or modify directly

gitlab doc looks pretty good to me. Lot's of great examples to work from.

… mucalc

yucongalicechen · 2024-12-26T20:30:17Z

thanks @bobleesj the link is very helpful and very clear to me. I edited the test comments. let me know if anything is unclear!
@sbillinge now ready for another review

sbillinge

please see inline comments. ATM I am just reviewing tests until we get them sorted. I don't really know what "standard density", and it doesn't make too much sense to me, so could you elaborate on that?

sbillinge · 2024-12-26T21:57:12Z

+ ],
+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
+ actual_mu = compute_mu_using_xraydb(


here you put
def test_compute_mu_using_xraydb(inputs, expected_mu): actual_mu = compute_mu_using_xraydb(**inputs)
which will unpack the input dict. You may have to handle the required args differently, but you can then have input_args and input_kwargs in your paramatrize and unpack them differently.

sbillinge · 2024-12-26T21:59:49Z

+ "inputs, expected_mu",
+ [
+ # Test whether the function returns the correct mu
+ ( # C1: No density or packing fraction provided, expect to compute mu based on standard density


do we want to allow this? what is "standard density"?

Just density I think - density under the standard conditions. So user can specify either a measured density or packing fraction.

The reason I'm not putting a strict "and/or" for density and packing fraction is that xraydb does not know the density to some materials like ZrO2. In this case user needs to put a density and a packing fraction, or they can put their measured density.

I see, so density is in the database? that is unexpected.

how does xraydb compute the density?

I see, it has a database of some standard materials. So we will need tests for cases where the material can be found and cases where it can't. How many different materials are in that database? The examples show just a few satandard materials (Kapton, quartz, etc.). Is it an extensive database or just a few x-ray standards?

How will you compute it for the cases where it is not in the db?

They have densities for some materials (for example, this returns sample name and density: https://xraypy.github.io/XrayDB/python.html#xraydb.get_materials).
I just reread their docstring and their density refers to the material density, not mass density: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.

sbillinge

Please see inline comments.

Also, this is conflicted

sbillinge · 2024-12-26T23:05:38Z

+ "inputs, expected_mu",
+ [
+ # Test whether the function returns the correct mu
+ ( # C1: No density or packing fraction provided, expect to compute mu based on standard density


I see, it has a database of some standard materials. So we will need tests for cases where the material can be found and cases where it can't. How many different materials are in that database? The examples show just a few satandard materials (Kapton, quartz, etc.). Is it an extensive database or just a few x-ray standards?

sbillinge · 2024-12-26T23:06:01Z

+ "inputs, expected_mu",
+ [
+ # Test whether the function returns the correct mu
+ ( # C1: No density or packing fraction provided, expect to compute mu based on standard density


How will you compute it for the cases where it is not in the db?

yucongalicechen · 2024-12-27T01:45:28Z

Please see inline comments.
Also, this is conflicted

So I think it only has density of pure elements and common compounds. I used get_materials to print out the list - it's pretty short.

I read through material_mu here: https://github.com/xraypy/XrayDB/blob/master/python/xraydb/materials.py. It uses a weighted sum approach for unknown materials. Here's the related code:

mass_tot, mu = 0.0, 0.0
for elem, frac in chemparse(formula).items():
mass = frac * atomic_mass(elem)
mu += mass * mu_elam(elem, energy, kind=kind) # mu_elam is the mu for the given element
mass_tot += mass
return density*mu/mass_tot

It looks like it's using mass density so we're good. I'll solve the conflict and add more tests for unknown materials.

yucongalicechen · 2024-12-27T03:06:26Z

+ sample_composition : str
+ The chemical formula or the name of the material.
+ energy : float
+ The energy in keV.


change unit to keV

"The energy of the incident x-rays in keV"

yucongalicechen · 2024-12-27T03:06:34Z

+
+ Computes mu based on the sample composition and energy.
+ User can provide a measured density or an estimated packing fraction.
+ Specifying the density is recommended, though not required for some pure or standard materials.


edit docstring

I think using xrayDB functionality here is not useful. The number of materials is so small, so there is no point to offer this to users as an option. It will just confuse them.
We could offer other approaches:
given a composition, try and get density from COD or Materials Project. For different polymorphs the densities will be different for the same composition, so we would have to handle that.
as a fallback, use a "best effort" atomic density (most tightly packed materials are around 5x10^22 cm^-3)? This would be "magic" which we don't normally like, but if we use this fallback we could give a warning.

yucongalicechen · 2024-12-27T03:06:52Z

+ },
+ 0.5330,
+ ),
+ ( # 2. Unknown material


add unknown material for testing

yucongalicechen · 2024-12-27T03:07:42Z

@sbillinge ready for another review

bobleesj · 2024-12-27T03:23:02Z

+ ],
+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
+ actual_mu = compute_mu_using_xraydb(**inputs)


this is beautiful. thanks! @yucongalicechen

sbillinge

please see inline comments.

sbillinge · 2024-12-27T11:07:13Z

 return metadata
+
+
+def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):


I think setting to None is clearer here. The logic from the perspective of the user is that we either have a packing fraction or we don't. If it is None, you can set it to 1 in the code.

sbillinge · 2024-12-27T11:08:10Z

 return metadata
+
+
+def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):


Also, didn't we discuss to change the name to sample_mass_density?

sbillinge · 2024-12-27T11:16:49Z

+
+ Computes mu based on the sample composition and energy.
+ User can provide a measured density or an estimated packing fraction.
+ Specifying the density is recommended, though not required for some pure or standard materials.


I think using xrayDB functionality here is not useful. The number of materials is so small, so there is no point to offer this to users as an option. It will just confuse them.
We could offer other approaches:
given a composition, try and get density from COD or Materials Project. For different polymorphs the densities will be different for the same composition, so we would have to handle that.
as a fallback, use a "best effort" atomic density (most tightly packed materials are around 5x10^22 cm^-3)? This would be "magic" which we don't normally like, but if we use this fallback we could give a warning.

sbillinge · 2024-12-27T11:17:27Z

+ sample_composition : str
+ The chemical formula or the name of the material.
+ energy : float
+ The energy in keV.


"The energy of the incident x-rays in keV"

sbillinge · 2024-12-27T11:22:11Z

+ },
+ 0.5330,
+ ),
+ ( # C2: Packing fraction (=0.5) provided only (only for known material)


reuse my pattern from C1 here.

sbillinge · 2024-12-27T11:23:09Z

+ },
+ 0.2665,
+ ),
+ ( # C3: Density provided only, expect to compute mu based on it


reuse my pattern above.

sbillinge · 2024-12-27T11:24:30Z

+ },
+ 1.252,
+ ),
+ ( # C4: Both density and packing fraction are provided, expect to compute mu based on both


this doesn't make any sense. It will result in two numbers, not one number. We probably want to raise an exception if both are provided.

sbillinge · 2024-12-27T11:25:11Z

+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
+ actual_mu = compute_mu_using_xraydb(**inputs)
+ assert actual_mu == pytest.approx(expected_mu, rel=0.01, abs=0.1)


this seems a bit too loose?

sbillinge · 2024-12-27T11:30:15Z

@yucongalicechen further to my review comments, I recommend not using the densities from the xrayDB at all and just computing using given densities. We can add another function that is get_density_from_cloud() or something that tries to get it from materials project or COD. This would require there to be a packing fraction specified, because the density we got from MP would be the fully dense density, so "material-density" not "sample-density"

yucongalicechen · 2024-12-27T15:10:08Z

@yucongalicechen further to my review comments, I recommend not using the densities from the xrayDB at all and just computing using given densities. We can add another function that is get_density_from_cloud() or something that tries to get it from materials project or COD. This would require there to be a packing fraction specified, because the density we got from MP would be the fully dense density, so "material-density" not "sample-density"

Just to clarify - this means user must enter density or packing fraction right? Something like what this is doing https://11bm.xray.aps.anl.gov/absorb/absorb.php? I can make another issue on getting density.

bobleesj · 2024-12-27T15:26:59Z

diffpy/diffpy.labpdfproc#146 (comment) - actually I meant to write this comment here in diffpy.utils @yucongalicechen

sbillinge · 2024-12-27T22:07:14Z

@yucongalicechen further to my review comments, I recommend not using the densities from the xrayDB at all and just computing using given densities. We can add another function that is get_density_from_cloud() or something that tries to get it from materials project or COD. This would require there to be a packing fraction specified, because the density we got from MP would be the fully dense density, so "material-density" not "sample-density"
Just to clarify - this means user must enter density or packing fraction right? Something like what this is doing https://11bm.xray.aps.anl.gov/absorb/absorb.php? I can make another issue on getting density.

Yes, either or and it triggers a different workflow.

yucongalicechen · 2024-12-28T02:23:29Z

+ "Warning: Density is set to None if a packing fraction is specified, "
+ "which may cause errors for some materials. "
+ "We recommend specifying sample mass density for now. "
+ "Auto-density calculation is coming soon."


add a warning message for now. I set density to None if user specifies packing fraction. We can probably replace this with density=get_density_from_cloud(sample_composition). There're some instructions here on how to estimate the density from given chemical formula: https://11bm.xray.aps.anl.gov/absorb/absorb.php. I can try to look into this more.

It's easy if we know the structure, but I am pretty sure MP has material density as an attribute so a simple API call will give it. We will have to add users adding their API key to the global config.....

Density is just number of atoms/unit cell volume which we know from composition and any CIF file we find, then converted to mass density with the formula, then multiplied by packing fraction

This code could be pretty reusable so I expect it will end up in diffpy.utils in the end (but in a future release)

yucongalicechen · 2024-12-28T02:25:21Z

@sbillinge ready for another review

sbillinge

please see inline comments.

Let's leave the "materials project/COD" workflow for v3.7.0

to correctly handle that, the best way is to define the functions and their signatures now (so the API desn't change when we implement it) but raise NotImplmentedError

Then wrap the line where the function is called wrap it in a try-except clause and handle the NotImplementedError, something like:

def get_density_from_the_cloud(composition, mp_token="":
"""
docstring with few words about intent and that it isn't implemented yet
""""
raise NotImplementedError
return

then let's say this function gets called in the code, we do this:

try:
material_density = get_density_from_cloud(composition) except NotImplementedError:
warning.warn("some helpful message about retrying using densiy")

This is a much tidier way of encapsulating what we need to change when we do actually implement it.

sbillinge · 2024-12-28T06:07:22Z

+ mu = material_mu(sample_composition, energy * 1000, density=sample_mass_density, kind="total") / 10
+ else:
+ warnings.warn(
+ "Warning: Density is set to None if a packing fraction is specified, "


You didn't need the word warning here. Warnings.warn handles that.

sbillinge · 2024-12-28T06:08:26Z

+ "Please rerun specifying only one."
+ )
+ if sample_mass_density is not None:
+ mu = material_mu(sample_composition, energy * 1000, density=sample_mass_density, kind="total") / 10


To make it more readable, don't hardcode numbers but rather variables with obvious names.

sbillinge · 2024-12-28T06:11:28Z

+ "Warning: Density is set to None if a packing fraction is specified, "
+ "which may cause errors for some materials. "
+ "We recommend specifying sample mass density for now. "
+ "Auto-density calculation is coming soon."


It's easy if we know the structure, but I am pretty sure MP has material density as an attribute so a simple API call will give it. We will have to add users adding their API key to the global config.....

sbillinge · 2024-12-28T06:13:21Z

+ "Warning: Density is set to None if a packing fraction is specified, "
+ "which may cause errors for some materials. "
+ "We recommend specifying sample mass density for now. "
+ "Auto-density calculation is coming soon."


Density is just number of atoms/unit cell volume which we know from composition and any CIF file we find, then converted to mass density with the formula, then multiplied by packing fraction

sbillinge · 2024-12-28T06:14:40Z

+ "Warning: Density is set to None if a packing fraction is specified, "
+ "which may cause errors for some materials. "
+ "We recommend specifying sample mass density for now. "
+ "Auto-density calculation is coming soon."


This code could be pretty reusable so I expect it will end up in diffpy.utils in the end (but in a future release)

yucongalicechen · 2024-12-29T04:37:02Z

+
+
+def get_density_from_cloud(sample_composition, mp_token=""):
+ """Function to get material density from the MP database.


add new function - not implemented

Do we want to also go to the COD database (doesn't require a token).

bobleesj · 2024-12-29T05:00:13Z

@yucongalicechen for future commit msgs/issues, could we try using this standard? (also aded to gitlab doc) scikit-package/scikit-package#212

sbillinge

Nice, thanks! Please see inline comments.

sbillinge · 2024-12-29T12:39:24Z

+
+
+def get_density_from_cloud(sample_composition, mp_token=""):
+ """Function to get material density from the MP database.


Do we want to also go to the COD database (doesn't require a token).

sbillinge · 2024-12-29T12:42:19Z

+ try:
+ sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
+ except NotImplementedError:
+ warnings.warn(


I think this needs to be an error not a warning, no? We need to interrupt execution.
Also, let's apologise... "So sorry, Density computation from composition is not implemented right now. We hope to have this implemented in the next release. Please rerun specifying a sample mass density.

Got it! I will add the COD database and change the error message

yucongalicechen · 2024-12-29T19:58:23Z

@yucongalicechen for future commit msgs/issues, could we try using this standard? (also aded to gitlab doc) Billingegroup/cookiecutter#212

thanks Bob! Will use that in my future commit messages

…tion

yucongalicechen · 2024-12-29T20:16:15Z

@sbillinge ready for another review! Thanks so much for the comments above.
I've added the MP/COD workflow in a new issue #286 following the new group standard

sbillinge

nice, thanks. Please see small inline comments

sbillinge · 2024-12-30T01:35:38Z

+ "inputs",
+ [
+ # Test when the function raises ValueError
+ # C1: Both mass density and packing fraction are provided


To compactify we want to write this as follows....also, put what you expect, e.g.,
# Test when the function has invalid inputs ( # C1: Both mass density and packing fraction are provided, expect ValueError exception { "sample_composition": "quartz", "energy": 10, "sample_mass_density": 2.65, "packing_fraction": 1, } ),

…d inputs

sbillinge

nearly there. Still trying to finalize the example for others.

sbillinge · 2024-12-30T02:23:37Z

+ # C1: Both mass density and packing fraction are provided, expect ValueError exception
+ (
+ {
+ "sample_composition": "quartz",


"quartz" is not a omposition, so we don't want this in the tests. It doesn't matter for the test, but let's not confuse readers. Please also fix this below. You can use SiO2 instead.
Also, please can you move the # C2 down a line inside the paren as I tried to illustrate before. thanks.

Ah gotcha. Will fix that

Ooops there're conflicts - willl fix it

sbillinge

please see inline

ghost · 2024-12-30T02:40:27Z

+ Parameters
+ ----------
+ sample_composition : str
+ The chemical formula or the name of the material.


not the name, just chemical formula.

ghost · 2024-12-30T02:41:10Z

+ energy : float
+ The energy of the incident x-rays in keV.
+ sample_mass_density : float, optional, Default is None
+ The mass density of the packed powder/sample in gr/cm^3.


g/cm*3, not gr/cm^3

ghost · 2024-12-30T04:27:56Z

nice @yucongalicechen !

yucongalicechenand others added 2 commits December 26, 2024 11:47

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add packing fraction, add more tests
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refine docstring and test comments
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Merge branch 'mucalc' of github.com:yucongalicechen/diffpy.utils into…
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… mucalc

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add xraydb function to compute muD diffpy/diffpy.labpdfproc#126
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merge from main and add tests for unknown materials
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feat: implement get_density_from_cloud() using MP/COD workflow #286
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enforce requirement to specify either density or packing fraction
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add notimplementederror
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refactor: rearrange error msg and docstring, update condition in func…
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fix: merge from main and fix conflicts
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yucongalicechen deleted the mucalc branch December 30, 2024 15:54

		return metadata


		def compute_mu_using_xraydb(sample, energy, density=None):

		assert actual_metadata == expected


		def test_compute_mu_using_xraydb():

		return metadata


		def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):



		def get_density_from_cloud(sample_composition, mp_token=""):
		"""Function to get material density from the MP database.

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yucongalicechen commented Dec 26, 2024•
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codecovBot commented Dec 26, 2024•
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bobleesjDec 26, 2024•
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yucongalicechen commented Dec 27, 2024•
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