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hruthhruth
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TESTS: added tester for 2ide ptycho data. It only checks the initial loading.
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2 files changed

+219
-2
lines changed

2 files changed

+219
-2
lines changed

‎src/pyxalign/io/loaders/lamni/api.py‎

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@@ -1,8 +1,7 @@
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from typing import Optional, Union
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from pyxalign.io.loaders.base import StandardData
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# from pyxalign.io.loaders.lamni.base_loader import BaseLoader
5-
BaseLoader=1
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from pyxalign.io.loaders.lamni.base_loader import BaseLoader
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from pyxalign.io.loaders.lamni.options import LamniLoadOptions
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from pyxalign.io.loaders.lamni.utils import load_experiment
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‎tests/full_tests/xrf_ptycho_1.py‎

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# this file currently only tests the pear v3 loader
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import os
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import argparse
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import multiprocessing as mp
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import cupy as cp
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import matplotlib.pyplot as plt
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import pyxalign
9+
from pyxalign import options as opts
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from pyxalign.api import enums
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from pyxalign.api.types import r_type
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from pyxalign.io.load import load_task
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from pyxalign.io.loaders.enums import LoaderType
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from pyxalign import gpu_utils
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from pyxalign.io.loaders.lamni.options import BaseLoadOptions, Beamline2IDELoadOptions
16+
from pyxalign.test_utils_2 import CITestArgumentParser, CITestHelper
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from pyxalign.api.options_utils import set_all_device_options
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import pyxalign.io.loaders
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from pyxalign.io.loaders.utils import convert_projection_dict_to_array
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def run_full_test_xrf_ptycho_1(
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update_tester_results: bool = False,
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save_temp_files: bool = False,
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test_start_point: enums.TestStartPoints = enums.TestStartPoints.BEGINNING,
26+
):
27+
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# Setup the test
29+
ci_options = opts.CITestOptions(
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test_data_name=os.path.join("2ide", "2025-1_Lamni-6"),
31+
update_tester_results=update_tester_results,
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proj_idx=list(range(0, 750, 150)),
33+
save_temp_files=save_temp_files,
34+
)
35+
ci_test_helper = CITestHelper(options=ci_options)
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# define a downscaling value for when volumes are saved to prevent
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# saving files large files
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# define a downscaling value for when volumes are saved to prevent
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# saving files large files
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s = 16
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# Setup default gpu options
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n_gpus = cp.cuda.runtime.getDeviceCount()
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gpu_list = list(range(0, n_gpus))
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single_gpu_device_options = opts.DeviceOptions()
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multi_gpu_device_options = opts.DeviceOptions(
47+
gpu=opts.GPUOptions(
48+
n_gpus=n_gpus,
49+
gpu_indices=gpu_list,
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chunk_length=20,
51+
)
52+
)
53+
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checkpoint_list = [enums.TestStartPoints.BEGINNING]
55+
if test_start_point in checkpoint_list:
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### Load ptycho input data ###
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# Define options for loading ptycho reconstructions
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base_load_options = BaseLoadOptions(
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loader_type=LoaderType.PEAR_V1,
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selected_experiment_name="",
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selected_sequences=[0],
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selected_ptycho_strings=[
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"Ndp64_LSQML_c12556_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7687_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7867_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12474_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7484_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12461_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12507_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12479_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12459_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7449_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8104_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7735_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12482_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7688_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12463_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7885_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7762_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12508_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12518_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12562_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12541_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12561_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7717_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7707_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12331_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12545_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12435_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12504_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12488_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12468_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12493_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7256_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7743_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12559_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12476_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12531_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7946_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12488_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7808_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12484_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12554_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12479_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12469_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7842_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12460_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7849_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12186_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12523_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12502_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12487_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12314_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12544_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12525_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
117+
"Ndp64_LSQML_c7381_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
118+
"Ndp64_LSQML_c7608_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
119+
"Ndp64_LSQML_c12480_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7804_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7773_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12515_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7561_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7716_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8035_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
126+
"Ndp64_LSQML_c12561_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12512_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12490_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12527_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7684_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
131+
"Ndp64_LSQML_c12442_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12533_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12562_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7933_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7828_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12471_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
137+
"Ndp64_LSQML_c12528_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12505_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12467_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7908_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12553_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8061_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12509_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12555_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7572_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12535_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7942_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12511_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12401_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12557_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12474_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7473_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12526_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8003_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7870_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12056_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8067_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8082_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12540_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12524_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c8044_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12500_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12560_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12457_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12481_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12558_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12552_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7916_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12485_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12516_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c7865_m0.5_gaussian_p10_mm_ic_pc_g_ul0.1/recon_Niter5000",
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"Ndp64_LSQML_c12492_m0.5_gaussian_p10_mm_ic_pc_ul0.1/recon_Niter5000",
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],
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scan_start=115,
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scan_end=264,
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)
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options = Beamline2IDELoadOptions(
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mda_folder=os.path.join(ci_test_helper.inputs_folder, "mda"),
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base=base_load_options,
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)
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# Load data
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standard_data = pyxalign.io.loaders.load_data_from_lamni_format(
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parent_projections_folder=os.path.join(ci_test_helper.inputs_folder, "ptychi_recons"),
185+
n_processes=int(mp.cpu_count() * 0.8),
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options=options,
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)
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w = 256
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new_shape = 576 + w, 832 + w
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projection_array = convert_projection_dict_to_array(
192+
standard_data.projections,
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delete_projection_dict=False,
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pad_with_mode=True,
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new_shape=new_shape,
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)
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198+
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scan_10 = standard_data.scan_numbers[10]
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ci_test_helper.save_or_compare_results(standard_data.probe, "standard_data_probe")
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ci_test_helper.save_or_compare_results(standard_data.scan_numbers, "standard_data_scan_numbers")
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ci_test_helper.save_or_compare_results(standard_data.angles, "standard_data_angles")
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ci_test_helper.save_or_compare_results(projection_array[10], "projection_array_10")
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ci_test_helper.save_or_compare_results(
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standard_data.probe_positions[scan_10], "probe_positions_10"
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)
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ci_test_helper.finish_test()
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if __name__ == "__main__":
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ci_parser = CITestArgumentParser()
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args = ci_parser.parser.parse_args()
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run_full_test_xrf_ptycho_1(
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update_tester_results=args.update_results,
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save_temp_files=args.save_temp_results,
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test_start_point=args.start_point,
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)

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