Start cleaning up with separating numba check from function usage

libeos/file_reader.py

@@ -20,11 +20,7 @@ from . import const
 from .header import Header
 from .instrument import Detector
 from .options import ExperimentConfig, IncidentAngle, MonitorType, ReaderConfig
-
-try:
-    from . import nb_helpers
-except Exception:
-    nb_helpers = None
+from .helpers import merge_frames, extract_walltime, filter_project_x, calculate_derived_properties_focussing
 
 # Time zone used to interpret time strings
 AMOR_LOCAL_TIMEZONE = zoneinfo.ZoneInfo(key='Europe/Zurich')
@@ -268,13 +264,7 @@ class AmorData:
         logging.debug(f'      => counting time {self.stopTime/1e9-self.startTime/1e9:8.2f} s')
 
     def extract_walltime(self, norm):
-        if nb_helpers:
-            self.wallTime_e = nb_helpers.extract_walltime(self.tof_e, self.dataPacket_p, self.dataPacketTime_p)
-        else:
-            self.wallTime_e = np.empty(np.shape(self.tof_e)[0], dtype=np.int64)
-            for i in range(len(self.dataPacket_p)-1):
-                self.wallTime_e[self.dataPacket_p[i]:self.dataPacket_p[i+1]] = self.dataPacketTime_p[i]
-            self.wallTime_e[self.dataPacket_p[-1]:] = self.dataPacketTime_p[-1]
+        self.wallTime_e = extract_walltime(self.tof_e, self.dataPacket_p, self.dataPacketTime_p)
         self.wallTime_e -= np.int64(self.seriesStartTime)
         logging.debug(f'      wall time from {self.wallTime_e[0]/1e9:6.1f} s to {self.wallTime_e[-1]/1e9:6.1f} s')
 
@@ -351,22 +341,13 @@ class AmorData:
     # TODO: - handle each neutron pulse individually, - associate with correct monitor also for slow neutrons
     def merge_time_frames(self):
         total_offset = self.tofCut + self.tau * (self.ch1TriggerPhase + self.chopperPhase/2)/180
-        if nb_helpers:
-            self.tof_e = nb_helpers.merge_frames(self.tof_e, self.tofCut, self.tau, total_offset)
-        else:
-            self.tof_e = np.remainder(self.tof_e-(self.tofCut-self.tau), self.tau)+total_offset  # tof shifted to 1 frame
+        self.tof_e = merge_frames(self.tof_e, self.tofCut, self.tau, total_offset)
 
     def filter_project_x(self):
         pixelLookUp = self.resolve_pixels()
-        if nb_helpers:
-            (self.detZ_e, self.detXdist_e, self.delta_e, self.mask_e) = nb_helpers.filter_project_x(
-                    pixelLookUp, self.pixelID_e.astype(np.int64), self.config.yRange[0], self.config.yRange[1]
-                    )
-        else:
-            # resolve pixel ID into y and z indicees, x position and angle
-            (detY_e, self.detZ_e, self.detXdist_e, self.delta_e) = pixelLookUp[np.int_(self.pixelID_e)-1, :].T
-            # define mask and filter y range
-            self.mask_e = (self.config.yRange[0]<=detY_e) & (detY_e<=self.config.yRange[1])
+        (self.detZ_e, self.detXdist_e, self.delta_e, self.mask_e) = filter_project_x(
+                pixelLookUp, self.pixelID_e.astype(np.int64), self.config.yRange[0], self.config.yRange[1]
+                )
 
     def correct_for_chopper_opening(self):
         # correct tof for beam size effect at chopper:  t_cor = (delta / 180 deg) * tau
@@ -378,9 +359,8 @@ class AmorData:
 
     def calculate_derived_properties(self):
         self.lamdaMax = const.lamdaCut+1.e13*self.tau*const.hdm/(self.chopperDetectorDistance+124.)
-        #if nb_helpers:
         if False:
-            self.lamda_e, self.qz_e, self.mask_e = nb_helpers.calculate_derived_properties_focussing(
+            self.lamda_e, self.qz_e, self.mask_e = calculate_derived_properties_focussing(
                     self.tof_e, self.detXdist_e, self.delta_e, self.mask_e,
                     self.config.lambdaRange[0], self.config.lambdaRange[1], self.nu, self.mu,
                     self.chopperDetectorDistance, const.hdm

libeos/helpers.py

@@ -0,0 +1,10 @@
+"""
+Helper functions used during calculations. Uses numba enhanced functions if available, otherwise numpy based
+fallback is imported.
+"""
+
+try:
+    from .helpers_numba import merge_frames, extract_walltime, filter_project_x, calculate_derived_properties_focussing
+except ImportError:
+    from .helpers_fallback import merge_frames, extract_walltime, filter_project_x, calculate_derived_properties_focussing
+

libeos/helpers_fallback.py

@@ -0,0 +1,26 @@
+"""
+Equivalent function as in helpers_numba.py but using just numpy functionality.
+"""
+
+import numpy as np
+
+def merge_frames(tof_e, tofCut, tau, total_offset):
+    # tof shifted to 1 frame
+    return np.remainder(tof_e-(tofCut-tau), tau)+total_offset
+
+def extract_walltime(tof_e, dataPacket_p, dataPacketTime_p):
+    output = np.empty(np.shape(tof_e)[0], dtype=np.int64)
+    for i in range(len(dataPacket_p)-1):
+        output[dataPacket_p[i]:dataPacket_p[i+1]] = dataPacketTime_p[i]
+    output[dataPacket_p[-1]:] = dataPacketTime_p[-1]
+    return output
+
+def filter_project_x(pixelLookUp, pixelID_e, ymin, ymax):
+    (detY_e, detZ_e, detXdist_e, delta_e) = pixelLookUp[np.int_(pixelID_e)-1, :].T
+    # define mask and filter y range
+    mask_e = (ymin<=detY_e) & (detY_e<=ymax[1])
+    return (detY_e, detZ_e, detXdist_e, delta_e, mask_e)
+
+def calculate_derived_properties_focussing(tof_e, detXdist_e, delta_e, mask_e,
+                                           lmin, lmax, nu, mu, chopperDetectorDistance, hdm):
+    raise NotImplementedError("Only exists in numba implementation so far.")

libeos/options.py

@@ -11,37 +11,6 @@ import numpy as np
 
 import logging
 
-#class Defaults:
-    # fileIdentifier
-    #outputPath                  = '.'
-    #rawPath                     = ['.', path.join('.','raw'), path.join('..','raw'), path.join('..','..','raw')]
-    #year                        = datetime.now().year
-    #normalisationFileIdentifier = []
-    #normalisationMethod         = 'o'
-    #monitorType                 = 'auto'
-    # subtract
-    #outputName                  = "fromEOS"
-    #outputFormat                = ['Rqz.ort']
-    #incidentAngle               = 'alphaF'
-    #qResolution                 = 0.01
-    #timeSlize
-    #scale                       = [1]
-    # autoscale
-    #lambdaRange                 = [2., 15.]
-    #thetaRange                  = [-12., 12.]
-    #thetaRangeR                 = [-0.75, 0.75]
-    #yRange                      = [11, 41]
-    #qzRange                     = [0.005, 0.51]
-    #chopperSpeed                = 500
-    #chopperPhase                = 0.0
-    #chopperPhaseOffset          = -9.1
-    #muOffset                    = 0
-    #mu                          = 0
-    #nu                          = 0
-    #sampleModel                 = None
-    #lowCurrentThreshold         = 50
-    #
-
 @dataclass
 class CommandlineParameterConfig:
     argument: str # default parameter for command line resutign ins "--argument"

neos.py

@@ -1 +0,0 @@
-eos.py