Commit e4719bfe authored by McDonnell, Marshall's avatar McDonnell, Marshall
Browse files

Fixes for tests + added test fixtures

parent 187c2678

.dockerignore

+1 −0
Original line number Diff line number Diff line 
Dockerfile

*.sh

**/output/

run_gsas2.sh

deleted100755 → 0
+0 −28
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CIF=177063_P2_R-3m_NaNiFeMn111O2_CollCode177063.cif

INSTPRM=Aeris_Si_Exported_03062025.instprm

XYE=GSAS_Sim_NaNiFeMnO2_111.xye



TEST_DIR=${PWD}/tests/data



#IMAGE=savannah.ornl.gov/asrp/gsas2_refinement@sha256:b0c351a9b9624e12dba5653a84c4c84e5246ee9e807228635eb0e89da67eb11c

IMAGE=asrp-gsas2-refinement



docker build -t ${IMAGE} .



docker run \

    -v ${TEST_DIR}/${CIF}:/refinement/input.cif \

    -v ${TEST_DIR}/${XYE}:/refinement/input.xye \

    -v ${TEST_DIR}/${INSTPRM}:/refinement/input.instprm \

    -v ${PWD}/output:/app/portal \

    ${IMAGE} \

        pixi run python -m gsas2_refinement.gsas2_refinement \

        --cif-filenames /refinement/input.cif \

        --cif-filenames /refinement/input.cif /refinement/input.cif \

        --gsas-filename /refinement/input.xye \

        --instrument-params-filename /refinement/input.instprm \

        --bank-ids 0 \

        --xmin 30.0 \

        --xmax 110.0 \

        --refine-scale-off \

        --scale-factor 20. \

        --num-cycles 0

src/gsas2_refinement/run_gsas2_fit.py

+3 −6
Original line number Diff line number Diff line 
import matplotlib.pyplot as plt

import numpy as np

import os

import time

from typing import Union, Dict, Any



import GSASIIscriptable as G2sc

import numpy as np



# Callback functions

from GSASII import GSASIIscriptable as G2sc
@@ -35,7 +32,7 @@ def print_stats(gpx: G2sc.G2Project): 


    print("")



def plot_refinement(gpx: G2sc.G2Project):

def plot_refinement(gpx: G2sc.G2Project, directory="/app/portal"):

    for hist in gpx.histograms():

        x = np.array(hist.getdata("X"))

        y = np.array(hist.getdata("Yobs"))
@@ -43,7 +40,7 @@ def plot_refinement(gpx: G2sc.G2Project): 
        dy = np.array(hist.getdata("Residual"))

        bkg = np.array(hist.getdata("Background"))



    filename=f"/app/portal/out_{time.time()}.png"

    filename=os.path.join(directory, f"out_{time.time()}.png")

    fig,ax = plt.subplots()

    ax.plot(x, y, label="exp", color='black', marker='x')

    ax.plot(x, ycalc, label="refinement", color='red')

tests/conftest.py

+17 −4
Original line number Diff line number Diff line
@@ -18,13 +18,26 @@ def fixture__si_cif(test_data_dir: Path) -> Path: 
    return test_data_dir / "Si.cif"





@pytest.fixture(name="si_gsas")

def fixture__si_gsas(test_data_dir: Path) -> Path:

@pytest.fixture(name="si_neutron_gsas")

def fixture__si_neutron_gsas(test_data_dir: Path) -> Path:

    return test_data_dir / "NOMAD_Si.gsa"





@pytest.fixture(name="nomad_instrument_parameters")

def fixture__nomad_instrument_parameters(test_data_dir: Path) -> Path:

@pytest.fixture(name="nomad_neutron_instrument_parameters")

def fixture__nomad_neutron_instrument_parameters(test_data_dir: Path) -> Path:

    return test_data_dir / "NOMAD_2021A_sixbanks_Shifter_Si_640e.instprm"



@pytest.fixture(name="nanifemno2_cif")

def fixture__nanifemno2_cif(test_data_dir: Path) -> Path:

    return test_data_dir / "177063_P2_R-3m_NaNiFeMn111O2_CollCode177063.cif"



@pytest.fixture(name="nanifemno2_xray_gsas")

def fixture__nanifemno2_xray_gsas(test_data_dir: Path) -> Path:

    return test_data_dir / "GSAS_Sim_NaNiFeMnO2_111.xye"



@pytest.fixture(name="nanifemno2_xray_instrument_parameters")

def fixture__aeris_xray_instrument_parameters(test_data_dir: Path) -> Path:

    return test_data_dir / "Aeris_Si_Exported_03062025.instprm"

tests/test_run_gsas2_fit.py

+14 −20
Original line number Diff line number Diff line 
import logging

import os

from pathlib import Path



from gsas2_refinement.run_gsas2_fit import run_gsas2_fit



def _assert_outputs(output_path: Path, stem: str):

    assert (output_path / f"{stem}_initial.gpx").exists()

    assert (output_path / f"{stem}_refined.bak0.gpx").exists()

    assert (output_path / f"{stem}_refined.cif").exists()

    assert (output_path / f"{stem}_refined.gpx").exists()

    assert (output_path / f"{stem}_refined.lst").exists()



def test_gsas2_fit_single_phase(si_cif, si_gsas, nomad_instrument_parameters):



def test_gsas2_fit_nomad_neutron_si_single_phase(si_cif, si_neutron_gsas, nomad_neutron_instrument_parameters):

    output_stem = "si_output"

    output_path = Path(__file__).parent.resolve()

    stype = "N"

    bank = 5

    xmin = 5000

    xmax = 15000



    run_gsas2_fit(

        structure_paths = [si_cif],

        gsas_input_path = si_gsas,

        structure_path = [si_cif],

        gsas_input_path = si_neutron_gsas,

        instrument_params_path = nomad_instrument_parameters,

        output_stem_fn = output_stem,

        banks = bank,
@@ -24,23 +28,17 @@ def test_gsas2_fit_single_phase(si_cif, si_gsas, nomad_instrument_parameters): 
        output_path = output_path,

    )



    assert os.path.join(output_path, output_stem + "_initial.gpx")

    assert os.path.join(output_path, output_stem + "_refined.bak0.gpx")

    assert os.path.join(output_path, output_stem + "_refined.cif")

    assert os.path.join(output_path, output_stem + "_refined.gpx")

    assert os.path.join(output_path, output_stem + "_refined.lst")



    _assert_outputs(output_path, output_stem)



def test_gsas2_fit_multi_phase(si_cif, si_gsas, nomad_instrument_parameters):

def test_gsas2_fit_nomad_neutron_si_multi_phase(si_cif, si_neutron_gsas, nomad_neutron_instrument_parameters):

    output_stem = "si_output"

    output_path = Path(__file__).parent.resolve()

    stype = "N"

    bank = 5

    xmin = 5000

    xmax = 15000



    run_gsas2_fit(

        structure_paths = [si_cif, si_cif],

        structure_path = [si_cif, si_cif],

        gsas_input_path = si_gsas,

        instrument_params_path = nomad_instrument_parameters,

        output_stem_fn = output_stem,
@@ -50,8 +48,4 @@ def test_gsas2_fit_multi_phase(si_cif, si_gsas, nomad_instrument_parameters): 
        output_path = output_path,

    )



    assert os.path.join(output_path, output_stem + "_initial.gpx")

    assert os.path.join(output_path, output_stem + "_refined.bak0.gpx")

    assert os.path.join(output_path, output_stem + "_refined.cif")

    assert os.path.join(output_path, output_stem + "_refined.gpx")

    assert os.path.join(output_path, output_stem + "_refined.lst")
 
 No newline at end of file
 
    _assert_outputs(output_path, output_stem)