Refactor: break the 3 module couplings blocking a clean forward/inverse split

test_angular_2v.py

@@ -12,7 +12,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 
 
 def test_arts2d_forward_pass():

test_arts2v_random.py

@@ -17,7 +17,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams, get_filter_spec
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 
 
 def _dump_ts_params(td: str, dist_type: str, ts_params: ThomsonParams, prefix: str = ""):

tests/test_forward/test_1d.py

@@ -11,7 +11,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams
-from tsadar.utils.data_handling.calibration import get_scattering_angles
+from tsadar.data.calibration import get_scattering_angles
 
 
 def test_1d_forward_pass():

tests/test_forward/test_angular_1v.py

@@ -11,7 +11,7 @@
 
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 
 
 def test_arts1d_forward_pass():

tests/test_forward/test_angular_2v.py

@@ -12,7 +12,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 
 
 def test_arts2d_forward_pass():

tests/test_inverse/test_1d_random.py

@@ -15,7 +15,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams, get_filter_spec
-from tsadar.utils.data_handling.calibration import get_scattering_angles
+from tsadar.data.calibration import get_scattering_angles
 
 
 def _perturb_params_(rng, params):

tests/test_inverse/test_angular_1v.py

@@ -20,7 +20,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams, get_filter_spec
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 from tsadar.inverse.loops import label
 
 def _dump_ts_params(td: str, ts_params: ThomsonParams, prefix: str = ""):

tests/test_inverse/test_angular_2v.py

@@ -17,7 +17,7 @@
 from tsadar.utils import misc
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from tsadar.core.modules.ts_params import ThomsonParams, get_filter_spec
-from tsadar.utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from tsadar.data.calibration import get_scattering_angles, get_calibrations
 
 
 def _dump_ts_params(td: str, dist_type: str, ts_params: ThomsonParams, prefix: str = ""):

tests/test_inverse/test_feature_detector.py

@@ -1,5 +1,5 @@
 from jax import config
-from tsadar.utils.process import prepare
+from tsadar.data import prepare
 
 config.update("jax_enable_x64", True)
 

tsadar/__init__.py

@@ -1,3 +1,3 @@
 from .runner import run_for_app
 from .core import ThomsonScatteringDiagnostic, ThomsonParams
-from .utils.data_handling.calibration import get_scattering_angles
+from .data.calibration import get_scattering_angles

tsadar/utils/data_handling/calibration.py → tsadar/data/calibration.py

@@ -3,7 +3,7 @@
 import scipy.io as sio
 import os
 
-BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "external")
+BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "external")
 
 
 def sa_lookup(beam):

tsadar/utils/process/correct_throughput.py → tsadar/data/correct_throughput.py

@@ -7,7 +7,7 @@
 import os
 import pandas as pd
 
-BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "external")
+BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "external")
 
 
 def correctThroughput(data, tstype, axisy, shotNum):

tsadar/utils/data_handling/data_visualizer.py → tsadar/data/data_visualizer.py

@@ -7,7 +7,7 @@
 from matplotlib.patches import Rectangle
 import tempfile, mlflow, os
 
-from tsadar.utils.process.lineouts import compute_lineout_pixel_indices
+from .lineouts import compute_lineout_pixel_indices
 
 
 def launch_data_visualizer(elecData, ionData, all_data, all_axes, config):

tsadar/utils/process/evaluate_background.py → tsadar/data/evaluate_background.py

@@ -6,7 +6,7 @@
 
 from scipy.signal import convolve2d as conv2
 
-from ..data_handling.load_ts_data import loadData
+from .load_ts_data import loadData
 from .correct_throughput import correctThroughput
 
 

tsadar/utils/process/lineouts.py → tsadar/data/lineouts.py

@@ -3,7 +3,7 @@
 from collections import defaultdict
 
 import numpy as np
-from tsadar.utils.process.evaluate_background import get_lineout_bg
+from .evaluate_background import get_lineout_bg
 
 
 def compute_lineout_pixel_indices(config, axisxE, axisxI, shift_zero, IAWtime, type_name="lineouts"):

tsadar/utils/data_handling/load_ts_data.py → tsadar/data/load_ts_data.py

@@ -3,9 +3,9 @@
 import os
 import numpy as np
 from scipy.signal import find_peaks
-from tsadar.utils.process.warpcorr import perform_warp_correction
+from .warpcorr import perform_warp_correction
 
-BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "external")
+BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "external")
 
 
 def _import_pyhdf():

tsadar/utils/process/prepare.py → tsadar/data/prepare.py

@@ -4,12 +4,12 @@
 import os
 
 from .evaluate_background import get_shot_bg
-from ..data_handling.load_ts_data import loadData
+from .load_ts_data import loadData
 from .correct_throughput import correctThroughput
-from ..data_handling.calibration import get_calibrations, get_scattering_angles
+from .calibration import get_calibrations, get_scattering_angles
 from .lineouts import get_lineouts
-from ..data_handling.data_visualizer import launch_data_visualizer
-from tsadar.utils.process.feature_detector import first_guess
+from .data_visualizer import launch_data_visualizer
+from .feature_detector import first_guess
 
 
 def prepare_data(config: Dict, shotNum: int) -> Dict:

tsadar/utils/process/warpcorr.py → tsadar/data/warpcorr.py

@@ -3,7 +3,7 @@
 import math, os
 from os.path import join, exists
 
-BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "external")
+BASE_FILES_PATH = os.path.join(os.path.dirname(__file__), "..", "external")
 
 
 def perform_warp_correction(warpedData, instrument="EPW", sweepSpeed=5, flatField=True):

tsadar/forward/calc_series.py

@@ -13,7 +13,7 @@
 from ..utils.plotting import plotters
 from ..core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from ..core.modules.ts_params import ThomsonParams
-from ..utils.data_handling.calibration import get_scattering_angles, get_calibrations
+from ..data.calibration import get_scattering_angles, get_calibrations
 
 
 def forward_pass(config):

tsadar/forward/calc_vs_data.py → tsadar/inverse/calc_vs_data.py

@@ -5,9 +5,9 @@
 
 from ..core.thomson_diagnostic import ThomsonScatteringDiagnostic
 from ..core.modules.ts_params import ThomsonParams
-from ..inverse.fitter import _validate_inputs_, load_data_for_fitting
-from ..utils.data_handling.calibration import get_calibrations
-from ..inverse.loss_function import LossFunction
+from .fitter import _validate_inputs_, load_data_for_fitting
+from ..data.calibration import get_calibrations
+from .loss_function import LossFunction
 
 from plotly.subplots import make_subplots
 import plotly.graph_objects as go

tsadar/inverse/fitter.py

@@ -7,7 +7,8 @@
 
 from tsadar.inverse.loops import multirun_angular_optax, one_d_loop
 
-from ..utils.process import prepare, postprocess
+from ..data import prepare
+from . import postprocess
 
 
 def _validate_inputs_(config: Dict) -> Dict:

tsadar/utils/process/postprocess.py → tsadar/inverse/postprocess.py

@@ -9,9 +9,9 @@
 from equinox import filter_jit
 
 from tsadar.utils.plotting import plotters
-from tsadar.inverse.loss_function import LossFunction
+from .loss_function import LossFunction
 from tsadar.core.modules.ts_params import IonParams
-from tsadar.inverse.loops import one_d_loop
+from .loops import one_d_loop
 from tsadar.core.thomson_diagnostic import ThomsonScatteringDiagnostic
 
 

tsadar/runner.py

@@ -8,7 +8,7 @@
 from .inverse import fitter
 from .forward import calc_series
 from .utils import misc
-from .forward import calc_vs_data
+from .inverse import calc_vs_data
 
 if "BASE_TEMPDIR" in os.environ:
     BASE_TEMPDIR = os.environ["BASE_TEMPDIR"]