moreniius 0.2.0__tar.gz → 0.2.1__tar.gz

{moreniius-0.2.0/src/moreniius.egg-info → moreniius-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: moreniius
-Version: 0.2.0
+Version: 0.2.1
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -8,8 +8,8 @@ Description-Content-Type: text/markdown
 Requires-Dist: zenlog==1.1
 Requires-Dist: platformdirs==3.11
 Requires-Dist: importlib_metadata; python_version < "3.8"
-Requires-Dist: mccode-antlr[hdf5]==0.6.0
-Requires-Dist: nexusformat==1.0.2
+Requires-Dist: mccode-antlr[hdf5]==0.7.0
+Requires-Dist: nexusformat==1.0.6
 
 # moreniius
 A project to contain custom components required to use `eniius` to produce `NeXus Structure` `JSON` from `mccode-antlr` simulated instruments.

{moreniius-0.2.0 → moreniius-0.2.1}/pyproject.toml

@@ -8,8 +8,8 @@ dependencies = [
     'zenlog==1.1,',
     'platformdirs==3.11',
     "importlib_metadata; python_version<'3.8'",
-    'mccode-antlr[hdf5]==0.6.0',
-    'nexusformat==1.0.2'
+    'mccode-antlr[hdf5]==0.7.0',
+    'nexusformat==1.0.6'
 ]
 readme = "README.md"
 authors = [

{moreniius-0.2.0 → moreniius-0.2.1}/src/moreniius/additions.py

@@ -14,13 +14,15 @@ COMPONENT_TYPE_NAME_TO_NEXUS['ESS_butterfly'] = 'NXmoderator'
 # full detector during the readout-construction.
 BIFROST_DETECTOR_MODULES = {}
 
+BIFROST_DETECTOR_TOPIC = 'bifrost_detector'
+
 
 def readout_translator(instance):
     """BIFROST specific Readout Master, should be deprecated in favour of ReadoutCAEN"""
     from numpy import einsum, ndarray, array
     from nexusformat.nexus import NXdetector, NXcylindrical_geometry
     from .utils import ev44_event_data_group
-    stream = ev44_event_data_group(source='caen', topic='SimulatedEvents')
+    stream = ev44_event_data_group(source='caen', topic=BIFROST_DETECTOR_TOPIC)
 
     readout_pos, readout_rot = instance.obj.orientation.position_parts(), instance.obj.orientation.rotation_parts()
 
@@ -28,29 +30,47 @@ def readout_translator(instance):
     total = sum(counts)
     points = [geometry.vertices.shape[0] for _, _, geometry in BIFROST_DETECTOR_MODULES.values()]
     total_points = sum(points)
-    cylinders = ndarray((total, 3), dtype='int32')
-    vertices = ndarray((total_points, 3), dtype='float32')
+    all_cylinders = ndarray((total, 3), dtype='int32')
+    all_vertices = ndarray((total_points, 3), dtype='float32')
     detector_number = ndarray((total,), dtype='int32')
 
     offset = 0
 
     for module_pos, module_rot, geometry in BIFROST_DETECTOR_MODULES.values():
         # Find the vector and rotation matrix linking the two coordinate systems
-        v = instance.instr.expr2nx(tuple((readout_pos - module_pos).position()))  # this is a mccode-antlr Vector
-        R1 = array(instance.instr.expr2nx(tuple(module_rot.inverse().rotation()))).reshape((3, 3))
-        R2 = array(instance.instr.expr2nx(tuple(readout_rot.rotation()))).reshape((3, 3))
         #
-        verts = einsum('ij,kj->ki', R1, geometry.vertices)
-        verts = verts + v
-        verts = einsum('ij,kj->ki', R2, verts)
+        # - The geometry is defined in the module coordinate system, where any point is p' = (x', y', z').
+        # - There is a rotation matrix rot1 that relates a vector in _a_ global coordinate system to the module
+        #   Such that
+        #       x' = rot1 x_global
+        #   Or
+        #       x_global = rot1.inv() x'
+        # - Similarly, there is a rotation matrix rot2 that relates a vector in the same global coordinate system to
+        #   the readout's coordinate system.
+        #       x = rot2 x_global
+        # - In this global coordinate system, the module position and readout positions have a vector connecting them
+        #       v = p_module - p_readout
+        #
+        # - So, to express the geometry in the readout's coordinate system, we convert p' to the global coordinate
+        #   system, add the difference vector between the two coordinate systems, then convert the result to the
+        #   readout coordinate system:
+        #       p = rot2 (v + rot1.inv() p')
+        #
+        v = instance.instr.expr2nx(tuple((module_pos - readout_pos).position()))  # this is a mccode-antlr Vector
+        rot1 = array(instance.instr.expr2nx(tuple(module_rot.inverse().rotation()))).reshape((3, 3))
+        rot2 = array(instance.instr.expr2nx(tuple(readout_rot.rotation()))).reshape((3, 3))
+        #
+        vertices = einsum('ij,kj->ki', rot1, geometry.vertices)
+        vertices = vertices + v
+        vertices = einsum('ij,kj->ki', rot2, vertices)
         #
-        cyls = offset + geometry.cylinders
-        vertices[offset:(offset + verts.shape[0])] = verts
-        cylinders[geometry.detector_number - 1, :] = cyls
+        cylinders = offset + geometry.cylinders
+        all_vertices[offset:(offset + vertices.shape[0])] = vertices
+        all_cylinders[geometry.detector_number - 1, :] = cylinders
         detector_number[geometry.detector_number - 1] = geometry.detector_number
-        offset += verts.shape[0]
+        offset += vertices.shape[0]
 
-    geometry = NXcylindrical_geometry(vertices=vertices, cylinders=cylinders, detector_number=detector_number)
+    geometry = NXcylindrical_geometry(vertices=all_vertices, cylinders=all_cylinders, detector_number=detector_number)
 
     return NXdetector(data=stream, geometry=geometry)
 
@@ -158,22 +178,25 @@ def detector_tubes_offsets_and_one_cylinder(self):
 
     halfi = (width - 2 * radius) / 2
     di = np.linspace(-halfi, halfi, ni)
-    dj = np.linspace(-height / 2, height / 2, nj)
+
+    half_pixel = height / (nj + 1) / 2  # half the size of one pixel along the tube
+    dj = -np.linspace(-height / 2 + half_pixel, height / 2 - half_pixel, nj)
     Dj, Di = np.meshgrid(dj, di)
 
     arc, triplet = analyzer - 1, cassette - 1  # naming from ICD 01 v6 indexing of triplets
 
     diameter = f'2 * {radius}' if isinstance(radius, str) else 2 * radius
 
-    pars['detector_number'] = [[pixel_fun(nj, arc, triplet, tube, position) for position in range(nj)] for tube in
-                               range(ni)]
-    pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), 'SimulatedEvents')
+    detector_number = [[pixel_fun(nj, arc, triplet, tube, position) for position in range(nj)] for tube in range(ni)]
+
+    pars['detector_number'] = np.array(detector_number).astype('int32')
+    pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), BIFROST_DETECTOR_TOPIC)
     pars['x_pixel_offset'] = NXfield(Di, units='m')
     pars['y_pixel_offset'] = NXfield(Dj, units='m')
     pars['x_pixel_size'] = NXfield(diameter, units='m')
     pars['y_pixel_size'] = NXfield(height / nj, units='m')
     pars['diameter'] = NXfield(diameter, units='m')
-    pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series') else f'{ni} He3 tubes'
+    pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series', True) else f'{ni} He3 tubes'
 
     # use NXcylindrical_geometry to define the detectors, which requires:
     #   vertices - (i, 3) -- points relative to the detector position defining each cylinder in the detector
@@ -187,8 +210,7 @@ def detector_tubes_offsets_and_one_cylinder(self):
     #   detector_number: (k,) -- maps the cylinders in cylinder by index with a detector id
     #
     # We're allowed to specify a single cylinder then le the x/y/z_offset position that pixel repeatedly:
-    dy = (dj[1] - dj[0]) / 2
-    vertices = NXfield([[0, -dy, 0], [radius, -dy, 0], [0, dy, 0]], units='m')
+    vertices = NXfield([[0, -half_pixel, 0], [radius, -half_pixel, 0], [0, half_pixel, 0]], units='m')
     cylinders = [[0, 1, 2]]
     geometry = NXcylindrical_geometry(vertices=vertices, cylinders=cylinders)
 
@@ -240,7 +262,7 @@ def detector_tubes_offsets_and_one_cylinder(self):
 #     cylinders = [[k, k+1, k+2] for k in [tube * 2 * (nj + 1) + 2 * j for tube in range(ni) for j in range(nj)]]
 #     detector_number = [pixel_fun(nj, arc, triplet, tube, j) for tube in range(ni) for j in range(nj)]
 #
-#     pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), 'SimulatedEvents')
+#     pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), BIFROST_DETECTOR_TOPIC)
 #     pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series') else f'{ni} He3 tubes'
 #
 #     geometry = NXcylindrical_geometry(vertices=vertices, cylinders=cylinders, detector_number=detector_number)
@@ -272,8 +294,9 @@ def detector_tubes_only_cylinder(self):
     nj = self.nx_parameter('no')  # corresponds to 'height' and McStas 'y' axis
     width, height, radius = [self.nx_parameter(n) for n in ('width', 'height', 'radius')]
     halfi = (width - 2 * radius) / 2
+    # signs of di and dj verified by examining plots of detector positions
     di = np.linspace(-halfi, halfi, ni)
-    dj = np.linspace(-height / 2, height / 2, nj+1)
+    dj = -np.linspace(-height / 2, height / 2, nj+1)
 
     # use NXcylindrical_geometry to define the detectors, which requires:
     #   vertices - (i, 3) -- points relative to the detector position defining each cylinder in the detector
@@ -290,10 +313,11 @@ def detector_tubes_only_cylinder(self):
     arc, triplet = analyzer - 1, cassette - 1  # naming from ICD 01 v6 indexing of triplets
 
     vertices = NXfield([v for x in di for y in dj for v in [[x, y, 0], [x, y, radius]]], units='m')
-    cylinders = [[k, k+1, k+2] for k in [tube * 2 * (nj + 1) + 2 * j for tube in range(ni) for j in range(nj)]]
-    detector_number = [pixel_fun(nj, arc, triplet, tube, j) for tube in range(ni) for j in range(nj)]
+    cylinders = np.array([[k, k+1, k+2] for k in [tube * 2 * (nj + 1) + 2 * j for tube in range(ni) for j in range(nj)]]).astype('int32')
+    detector_number = np.array([pixel_fun(nj, arc, triplet, tube, j) for tube in range(ni) for j in range(nj)]).astype('int32')
 
-    pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series') else f'{ni} He3 tubes'
+    pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), BIFROST_DETECTOR_TOPIC)
+    pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series', True) else f'{ni} He3 tubes'
 
     geometry = NXcylindrical_geometry(vertices=vertices, cylinders=cylinders, detector_number=detector_number)
 
@@ -302,13 +326,16 @@ def detector_tubes_only_cylinder(self):
             from nexusformat.nexus import NXdata
             from moreniius.utils import NotNXdict
             from json import loads
-            pars['data'] = NXdata(data=NotNXdict(loads(md.value)))
+            stream = loads(md.value)
+            name = stream.get('module', 'metadata')
+            pars[name] = NXdata(data=NotNXdict(stream))
 
     return NXdetector(**pars, geometry=geometry)
 
 
 def bifrost_detector_collector(self):
-    nx_obj = detector_tubes_only_cylinder(self)
+    # nx_obj = detector_tubes_only_cylinder(self)  # each pixel is a cylinder
+    nx_obj = detector_tubes_offsets_and_one_cylinder(self)  # all pixels share one cylinder
     # stash the object parts
     pos, rot = self.obj.orientation.position_parts(), self.obj.orientation.rotation_parts()
     BIFROST_DETECTOR_MODULES[str(self.obj.when)] = pos, rot, nx_obj.geometry
@@ -326,16 +353,17 @@ def bifrost_detector_collector(self):
 #
 #     # parameters to be filled-in
 #     pars = {}
-#     # pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), 'SimulatedEvents')
+#     # pars['data'] = ev44_event_data_group(bifrost_source_20230704(arc, triplet), BIFROST_DETECTOR_TOPIC)
 #     # pars['type'] = f'{ni} He3 tubes in series' if self.nx_parameter('wires_in_series') else f'{ni} He3 tubes'
 #     pars['geometry'] = geometry.to_nexus()
 #     return NXmonitor(**pars)
 
 
 # Patch-in the new methods
-register_translator('Readout', readout_translator)
+# register_translator('Readout', readout_translator)
 register_translator('Monochromator_Rowland', monochromator_rowland_translator)
 register_translator('Detector_tubes', bifrost_detector_collector)
+register_translator('Detector_time_tubes', bifrost_detector_collector)
 register_translator('Frame_monitor', monitor_translator)
 
 log.debug('moreniius.mccode.NXInstance translators extended')

{moreniius-0.2.0 → moreniius-0.2.1}/src/moreniius/mccode/comp.py

@@ -118,6 +118,8 @@ def elliptic_guide_gravity_translator(nxinstance):
         z = x * p['l']
         vertices.extend([[-w, -h, z], [-w, h, z], [w, h, z], [w, -h, z]])
 
+    # These are only the guide faces (that is, the inner faces of the sides of the guide housing)
+    # The entry and exit are not guide faces and therefore are NOT represented here!
     for i in range(n):
         j0, j1, j2, j3, j4, j5, j6, j7 = [4 * i + k for k in range(8)]
         faces.extend([[j0, j1, j5, j4], [j1, j2, j6, j5], [j2, j3, j7, j6], [j3, j0, j4, j7]])

{moreniius-0.2.0 → moreniius-0.2.1}/src/moreniius/mccode/instance.py

@@ -71,7 +71,7 @@ class NXInstance:
     nx: Union[None, dict, NXfield] = None
     dump_mcstas: bool = False
 
-    def parameter(self, name):
+    def parameter(self, name, default=None):
         """
         Pull out a named instance parameter -- if it's value is not a constant, attempt to evaluate it
         using the Instr declare and initialize sections
@@ -79,7 +79,7 @@ class NXInstance:
         par = self.obj.get_parameter(name)
         if par is None:
             log.warn(f'It appears that {self.obj.type.name} does not define the parameter {name}')
-            return None
+            return default
 
         expr = par.value
         # log.info(f'get parameter {name} which is {par}  and expr {repr(expr)}')
@@ -100,9 +100,9 @@ class NXInstance:
     def expr2nx(self, expr: Expr):
         return self.instr.expr2nx(expr)
 
-    def nx_parameter(self, name):
+    def nx_parameter(self, name, default=None):
         """Retrieve the named instance parameter and convert to a NeXus compatible value"""
-        return self.expr2nx(self.parameter(name))
+        return self.expr2nx(self.parameter(name, default))
 
     def make_nx(self, nx_class, *args, **kwargs):
         return self.instr.make_nx(nx_class, *args, **kwargs)

{moreniius-0.2.0 → moreniius-0.2.1/src/moreniius.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: moreniius
-Version: 0.2.0
+Version: 0.2.1
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -8,8 +8,8 @@ Description-Content-Type: text/markdown
 Requires-Dist: zenlog==1.1
 Requires-Dist: platformdirs==3.11
 Requires-Dist: importlib_metadata; python_version < "3.8"
-Requires-Dist: mccode-antlr[hdf5]==0.6.0
-Requires-Dist: nexusformat==1.0.2
+Requires-Dist: mccode-antlr[hdf5]==0.7.0
+Requires-Dist: nexusformat==1.0.6
 
 # moreniius
 A project to contain custom components required to use `eniius` to produce `NeXus Structure` `JSON` from `mccode-antlr` simulated instruments.

{moreniius-0.2.0 → moreniius-0.2.1}/src/moreniius.egg-info/requires.txt

@@ -1,7 +1,7 @@
 zenlog==1.1
 platformdirs==3.11
-mccode-antlr[hdf5]==0.6.0
-nexusformat==1.0.2
+mccode-antlr[hdf5]==0.7.0
+nexusformat==1.0.6
 
 [:python_version < "3.8"]
 importlib_metadata

{moreniius-0.2.0 → moreniius-0.2.1}/tests/test_nexus_structure.py

@@ -6,9 +6,12 @@ class NexusStrctureTestCase(unittest.TestCase):
     def setUp(self):
         from json import dumps
         from mccode_antlr.loader import parse_mcstas_instr
-        from mccode_to_kafka.writer import nexus_structure, edge
-        m0 = nexus_structure('mon0', shape=[edge(10, 0.5, 10.5, 't', 'usec', 'monitor')])
-        m1 = nexus_structure('mon1', shape=[edge(10, 1.5, 11.5, 't', 'usec', 'monitor')])
+        from mccode_to_kafka.writer import da00_variable_config, da00_dataarray_config
+        t0 = {'name': 't', 'unit': 'usec', 'label': 'monitor', 'data': {'first': 0.5, 'last': 10.5, 'size': 11}}
+        t1 = {'name': 't', 'unit': 'usec', 'label': 'monitor', 'data': {'first': 1.5, 'last': 11.5, 'size': 11}}
+        m0 = da00_dataarray_config(topic='mon0', source='mccode-to-kafka', constants=[da00_variable_config(**t0)])
+        m1 = da00_dataarray_config(topic='mon1', source='mccode-to-kafka', constants=[da00_variable_config(**t1)])
+
         instr = f"""DEFINE INSTRUMENT chopper_spectrometer(
         ch1speed, ch2speed, ch1phase, ch2phase
         )