Merge pull request #69 from iguinn/main

Bug fixes

setup.cfg

@@ -41,7 +41,6 @@ install_requires =
     parse
     pint
     pyarrow
-    pyfftw
     scipy
     tqdm>=4.27
 python_requires = >=3.9

src/dspeed/processing_chain.py

@@ -783,12 +783,6 @@ def _parse_expr(
             else:
                 ProcessingChainError("only 1D arrays are supported: " + expr)
 
-        elif isinstance(node, ast.Num):
-            return node.n
-
-        elif isinstance(node, ast.Str):
-            return node.s
-
         elif isinstance(node, ast.Constant):
             return node.value
 

src/dspeed/processors/__init__.py

@@ -63,7 +63,6 @@
 from .convolutions import convolve_wf, fft_convolve_wf
 from .dwt import discrete_wavelet_transform
 from .energy_kernels import cusp_filter, dplms, zac_filter
-from .fftw import dft, inv_dft, psd
 from .fixed_time_pickoff import fixed_time_pickoff
 from .gaussian_filter1d import gaussian_filter1d
 from .get_multi_local_extrema import get_multi_local_extrema
@@ -115,9 +114,6 @@
     "t0_filter",
     "zac_filter",
     "discrete_wavelet_transform",
-    "dft",
-    "inv_dft",
-    "psd",
     "fixed_time_pickoff",
     "gaussian_filter1d",
     "get_multi_local_extrema",

src/dspeed/processors/time_point_thresh.py

@@ -371,10 +371,10 @@ def multi_time_point_thresh(
 
 @guvectorize(
     [
-        "void(float32[:], float32, float32, float32, float32, float32[:], float32[:])",
-        "void(float64[:], float64, float64, float64, float64, float64[:], float64[:])",
+        "void(float32[:], float32, float32, float32, float32, uint32[:], float32[:], float32[:])",
+        "void(float64[:], float64, float64, float64, float64, uint32[:], float64[:], float64[:])",
     ],
-    "(n),(),(),(),(),(m),(m)",
+    "(n),(),(),(),(),(),(m),(m)",
     **nb_kwargs,
 )
 def bi_level_zero_crossing_time_points(
@@ -383,6 +383,7 @@ def bi_level_zero_crossing_time_points(
     a_neg_threshold_in: float,
     gate_time_in: int,
     t_start_in: int,
+    n_crossings_out: int,
     polarity_out: np.array,
     t_trig_times_out: np.array,
 ) -> None:
@@ -403,6 +404,8 @@ def bi_level_zero_crossing_time_points(
         The number of samples that the next threshold crossing has to be within in order to count a 0 crossing
     t_start_in
         the starting index.
+    n_crossings_out
+        the number of zero-crossings found. Note: if there are more zeros than elements in output arrays, this will continue to increment but the polarity and trigger time will not be added to the output buffers
     polarity_out
         An array holding the polarity of identified pulses. 0 for negative and 1 for positive
     t_trig_times_out
@@ -418,7 +421,7 @@ def bi_level_zero_crossing_time_points(
         "trig_times_out": {
             "function": "multi_trigger_time",
             "module": "dspeed.processors",
-            "args": ["wf_rc_cr2", "5", "-10", 0, "polarity_out(20)", "trig_times_out(20)"],
+            "args": ["wf_rc_cr2", "5", "-10", 0, "n_crossings", "polarity_out(20, vector_len=n_crossings)", "trig_times_out(20, vector_len=n_crossings)"],
             "unit": "ns"
         }
     """
@@ -449,7 +452,7 @@ def bi_level_zero_crossing_time_points(
     is_above_thresh = False
     is_below_thresh = False
     crossed_zero = False
-    trig_array_idx = 0
+    n_crossings_out[0] = 0
     for i in range(int(t_start_in), len(w_in) - 1, 1):
         if is_below_thresh and (w_in[i] <= 0 < w_in[i + 1]):
             crossed_zero = True
@@ -459,9 +462,10 @@ def bi_level_zero_crossing_time_points(
         if w_in[i] <= a_pos_threshold_in < w_in[i + 1]:
             if crossed_zero and is_below_thresh:
                 if i - is_below_thresh < gate_time_in:
-                    t_trig_times_out[trig_array_idx] = neg_trig_time_candidate
-                    polarity_out[trig_array_idx] = 0
-                    trig_array_idx += 1
+                    if n_crossings_out[0] < len(polarity_out):
+                        t_trig_times_out[n_crossings_out[0]] = neg_trig_time_candidate
+                        polarity_out[n_crossings_out[0]] = 0
+                    n_crossings_out[0] += 1
                 else:
                     is_above_thresh = i
 
@@ -478,9 +482,10 @@ def bi_level_zero_crossing_time_points(
         if w_in[i] >= a_neg_threshold_in > w_in[i + 1]:
             if crossed_zero and is_above_thresh:
                 if i - is_above_thresh < gate_time_in:
-                    t_trig_times_out[trig_array_idx] = pos_trig_time_candidate
-                    polarity_out[trig_array_idx] = 1
-                    trig_array_idx += 1
+                    if n_crossings_out[0] < len(polarity_out):
+                        t_trig_times_out[n_crossings_out[0]] = pos_trig_time_candidate
+                        polarity_out[n_crossings_out[0]] = 1
+                    n_crossings_out[0] += 1
                 else:
                     is_below_thresh = i
                 is_above_thresh = False