Merge branch 'restructure-src-into-subdir'

Author: kaghi

scripts/s02_compute_metrics.py

@@ -9,7 +9,7 @@
 from plotly.subplots import make_subplots
 from tqdm.auto import tqdm
 
-from indeca.utils import norm
+from indeca.utils.utils import norm
 from tests.testing_utils.io import load_gt_ds, subset_gt_ds
 from tests.testing_utils.metrics import compute_metrics
 from tests.testing_utils.plotting import plot_traces

scripts/s03_make_figures.py

@@ -11,9 +11,9 @@
 from matplotlib.lines import Line2D
 from matplotlib.patches import ConnectionPatch, Rectangle
 
-from indeca.AR_kernel import estimate_coefs, solve_fit_h_num
-from indeca.simulation import AR2exp, AR2tau, ar_pulse, eval_exp, find_dhm
-from indeca.utils import norm
+from indeca.core.AR_kernel import estimate_coefs, solve_fit_h_num
+from indeca.core.simulation import AR2exp, AR2tau, ar_pulse, eval_exp, find_dhm
+from indeca.utils.utils import norm
 from tests.conftest import fixt_deconv
 from tests.testing_utils.compose import GridSpec
 from tests.testing_utils.io import load_gt_ds, subset_gt_ds

src/indeca/__init__.py

@@ -1,3 +1,3 @@
-from .logging_config import set_package_log_level
+from .utils.logging_config import set_package_log_level
 
 __all__ = ["set_package_log_level"]

src/indeca/config.py

@@ -9,8 +9,8 @@
 from scipy.optimize import curve_fit
 from statsmodels.tsa.stattools import acovf
 
-from indeca.deconv import construct_G, construct_R
-from indeca.simulation import AR2tau, ar_pulse, solve_p, tau2AR
+from indeca.core.deconv.deconv import construct_G, construct_R
+from indeca.core.simulation import AR2tau, ar_pulse, solve_p, tau2AR
 
 
 def convolve_g(s, g):

src/indeca/AR_kernel.py src/indeca/core/AR_kernel.pysrc/indeca/AR_kernel.py renamed to src/indeca/core/AR_kernel.py

@@ -0,0 +1,3 @@
+from .deconv import DeconvBin, construct_R, construct_G, max_thres, sum_downsample
+
+__all__ = ["DeconvBin", "construct_R", "construct_G", "max_thres", "sum_downsample"]

src/indeca/core/__init__.py

@@ -14,9 +14,9 @@
 from scipy.signal import ShortTimeFFT, find_peaks
 from scipy.special import huber
 
-from indeca.logging_config import get_module_logger
-from indeca.simulation import AR2tau, ar_pulse, exp_pulse, solve_p, tau2AR
-from indeca.utils import scal_lstsq
+from indeca.utils.logging_config import get_module_logger
+from indeca.core.simulation import AR2tau, ar_pulse, exp_pulse, solve_p, tau2AR
+from indeca.utils.utils import scal_lstsq
 
 # Initialize logger for this module
 logger = get_module_logger("deconv")
@@ -102,7 +102,9 @@ def bin_convolve(
     out = np.zeros(s_len)
     nzidx = np.where(s)[0]
     if nzidx_s is not None:
-        nzidx = nzidx_s[nzidx]
+        nzidx = nzidx_s[nzidx].astype(
+            np.int64
+        )  # astype to fix numpa issues on GPU on Windows
     for i0 in nzidx:
         i1 = min(i0 + coef_len, s_len)
         clen = i1 - i0
@@ -231,8 +233,8 @@ def __init__(
         self.Hlim = Hlim
         self.dashboard = dashboard
         self.dashboard_uid = dashboard_uid
-        self.nzidx_s = np.arange(self.T)
-        self.nzidx_c = np.arange(self.T)
+        self.nzidx_s = np.arange(self.T, dtype=np.int64)
+        self.nzidx_c = np.arange(self.T, dtype=np.int64)
         self.x_cache = None
         self.err_weighting = err_weighting
         self.masking_r = masking_radius

src/indeca/core/deconv/__init__.py

@@ -0,0 +1,3 @@
+from .dashboard import Dashboard
+
+__all__ = ["Dashboard"]