python-microscopy · David-Baddeley · Sep 20, 2022 · Sep 7, 2022 · Sep 7, 2022 · Sep 7, 2022
diff --git a/PYME/Acquire/Hardware/Simulator/simcontrol.py b/PYME/Acquire/Hardware/Simulator/simcontrol.py
@@ -80,11 +80,18 @@ class RandomDistribution(HasTraits):
     n_instances = Int(1)
     region_size = Float(5000)
     generator = Instance(HasTraits)
+    # force one of the points to be at the origin (dirty hack to make sure there is a structure present in the simulator at startup)
+    force_at_origin = Bool(False) 
 
     def points(self):
         xp = self.region_size*np.random.uniform(-1, 1, self.n_instances)
         yp = self.region_size*np.random.uniform(-1, 1, self.n_instances)
 
+        if self.force_at_origin:
+            xp[0] = 0.0
+            yp[0] = 0.0
+
+
         for xi, yi in zip(xp, yp):
             for p in self.generator.points():
                 p1 = np.copy(p)

diff --git a/PYME/Acquire/Scripts/init_sim_htsms.py b/PYME/Acquire/Scripts/init_sim_htsms.py
@@ -128,7 +128,7 @@ def sim_controls(MainFrame, scope):
     MainFrame.camPanels.append((msc, 'Simulation'))
 
     from PYME.simulation import pointsets
-    scope.simcontrol.point_gen = simcontrol.RandomDistribution(n_instances=25,region_size=70e3, 
+    scope.simcontrol.point_gen = simcontrol.RandomDistribution(n_instances=25,region_size=70e3, force_at_origin=True,
                                                                 generator=simcontrol.Group(generators=[pointsets.WiglyFibreSource(),
                                                                     simcontrol.AssignChannel(channel=1, generator=pointsets.SHNucleusSource())
                                                                     ]))

diff --git a/PYME/misc/pyme_zeroconf.py b/PYME/misc/pyme_zeroconf.py
@@ -21,72 +21,89 @@
 import time
 #import Pyro.core
 import threading
+import logging
+logger = logging.getLogger(__name__)
 
-class PatchedServiceInfo(zeroconf.ServiceInfo):
-    """
-    A patched version of the zero-conf ServiceInfo object which ensures that we get the port number as well as the address and name
-    """
-
-    def request(self, zc, timeout):
-        """Returns true if the service could be discovered on the
-        network, and updates this object with details discovered.
+if zeroconf.__version__ >= '0.35':
+    # new ServiceInfo class
+
+    class PatchedServiceInfo(zeroconf.ServiceInfo):
+        """
+        A patched version of the zero-conf ServiceInfo object which ensures that we get the port number as well as the address and name
         """
-        now = zeroconf.current_time_millis()
-        delay = zeroconf._LISTENER_TIME
-        next_ = now + delay
-        last = now + timeout
+        @property
+        def _is_complete(self) -> bool:
+            """The ServiceInfo has all expected properties."""
+            return bool(self.text is not None and self.port is not None and (self._ipv4_addresses or self._ipv6_addresses))
 
-        record_types_for_check_cache = [
-            (zeroconf._TYPE_SRV, zeroconf._CLASS_IN),
-            (zeroconf._TYPE_TXT, zeroconf._CLASS_IN),
-        ]
-        if self.server is not None:
-            record_types_for_check_cache.append((zeroconf._TYPE_A, zeroconf._CLASS_IN))
-        for record_type in record_types_for_check_cache:
-            cached = zc.cache.get_by_details(self.name, *record_type)
-            if cached:
-                self.update_record(zc, now, cached)
+else:
 
-        if None not in (self.server, self.address, self.text, self.port):
-            return True
+    logger.warning(f'using an old version of zeroconf ({zeroconf.__version__}), consider upgrading')
+    class PatchedServiceInfo(zeroconf.ServiceInfo):
+        """
+        A patched version of the zero-conf ServiceInfo object which ensures that we get the port number as well as the address and name
+        """
+
+        def request(self, zc, timeout):
+            """Returns true if the service could be discovered on the
+            network, and updates this object with details discovered.
+            """
+            now = zeroconf.current_time_millis()
+            delay = zeroconf._LISTENER_TIME
+            next_ = now + delay
+            last = now + timeout
 
-        try:
-            zc.add_listener(self, zeroconf.DNSQuestion(self.name, zeroconf._TYPE_ANY, zeroconf._CLASS_IN))
-            while None in (self.server, self.address, self.text, self.port):
-                if last <= now:
-                    return False
-                if next_ <= now:
-                    out = zeroconf.DNSOutgoing(zeroconf._FLAGS_QR_QUERY)
-                    out.add_question(
-                        zeroconf.DNSQuestion(self.name, zeroconf._TYPE_SRV, zeroconf._CLASS_IN))
-
-                    if self.port is not None:
-                        out.add_answer_at_time(
-                            zc.cache.get_by_details(
-                                self.name, zeroconf._TYPE_SRV, zeroconf._CLASS_IN), now)
-
-                    out.add_question(
-                        zeroconf.DNSQuestion(self.name, zeroconf._TYPE_TXT, zeroconf._CLASS_IN))
-                    out.add_answer_at_time(
-                        zc.cache.get_by_details(
-                            self.name, zeroconf._TYPE_TXT, zeroconf._CLASS_IN), now)
-
-                    if self.server is not None:
+            record_types_for_check_cache = [
+                (zeroconf._TYPE_SRV, zeroconf._CLASS_IN),
+                (zeroconf._TYPE_TXT, zeroconf._CLASS_IN),
+            ]
+            if self.server is not None:
+                record_types_for_check_cache.append((zeroconf._TYPE_A, zeroconf._CLASS_IN))
+            for record_type in record_types_for_check_cache:
+                cached = zc.cache.get_by_details(self.name, *record_type)
+                if cached:
+                    self.update_record(zc, now, cached)
+
+            if None not in (self.server, self.address, self.text, self.port):
+                return True
+
+            try:
+                zc.add_listener(self, zeroconf.DNSQuestion(self.name, zeroconf._TYPE_ANY, zeroconf._CLASS_IN))
+                while None in (self.server, self.address, self.text, self.port):
+                    if last <= now:
+                        return False
+                    if next_ <= now:
+                        out = zeroconf.DNSOutgoing(zeroconf._FLAGS_QR_QUERY)
+                        out.add_question(
+                            zeroconf.DNSQuestion(self.name, zeroconf._TYPE_SRV, zeroconf._CLASS_IN))
+
+                        if self.port is not None:
+                            out.add_answer_at_time(
+                                zc.cache.get_by_details(
+                                    self.name, zeroconf._TYPE_SRV, zeroconf._CLASS_IN), now)
+
                         out.add_question(
-                            zeroconf.DNSQuestion(self.server, zeroconf._TYPE_A, zeroconf._CLASS_IN))
+                            zeroconf.DNSQuestion(self.name, zeroconf._TYPE_TXT, zeroconf._CLASS_IN))
                         out.add_answer_at_time(
                             zc.cache.get_by_details(
-                                self.server, zeroconf._TYPE_A, zeroconf._CLASS_IN), now)
-                    zc.send(out)
-                    next_ = now + delay
-                    delay *= 2
-
-                zc.wait(min(next_, last) - now)
-                now = zeroconf.current_time_millis()
-        finally:
-            zc.remove_listener(self)
+                                self.name, zeroconf._TYPE_TXT, zeroconf._CLASS_IN), now)
+
+                        if self.server is not None:
+                            out.add_question(
+                                zeroconf.DNSQuestion(self.server, zeroconf._TYPE_A, zeroconf._CLASS_IN))
+                            out.add_answer_at_time(
+                                zc.cache.get_by_details(
+                                    self.server, zeroconf._TYPE_A, zeroconf._CLASS_IN), now)
+                        zc.send(out)
+                        next_ = now + delay
+                        delay *= 2
+
+                    zc.wait(min(next_, last) - now)
+                    now = zeroconf.current_time_millis()
+            finally:
+                zc.remove_listener(self)
 
-        return True
+            return True
 
 class ZCListener(object): 
     def __init__(self, protocol='_pyme-pyro'):
@@ -115,7 +132,7 @@ def add_service(self, zc, _type, name):
 
         info = PatchedServiceInfo(_type, name)
         if info.request(zc, 5000):
-            if is_port_open(socket.inet_ntoa(info.address), info.port):
+            if is_port_open(socket.inet_ntoa(info.addresses[0]), info.port):
                 with self._lock:
                     #info = zc.get_service_info(_type, name)
                     self.advertised_services[nm] = info
@@ -142,7 +159,7 @@ def _poll_services_open(self):
             # check to see if the services are up (without lock)
             dead_svcs = []
             for name, info in svcs:
-                if not is_port_open(socket.inet_ntoa(info.address), info.port):
+                if not is_port_open(socket.inet_ntoa(info.addresses[0]), info.port):
                     dead_svcs.append((name, info))
 
             # delete any dead services
@@ -202,9 +219,9 @@ def register_service(self, name, address, port, desc={}):
             raise RuntimeError('Name "%s" already exists' %name)
 
         info = PatchedServiceInfo("%s._tcp.local." % self._protocol,
-                           "%s.%s._tcp.local." % (name, self._protocol),
-                           socket.inet_aton(address), port, 0, 0,
-                           desc)
+                           name="%s.%s._tcp.local." % (name, self._protocol),
+                           addresses=[socket.inet_aton(address),], port=port, weight=0, priority=0,
+                           properties=desc)
 
         self._services[name] = info
         self.zc.register_service(info)

diff --git a/PYME/recipes/base.py b/PYME/recipes/base.py
@@ -9,7 +9,7 @@
 #import wx
 import six
 
-from PYME.recipes.traits import HasTraits, Float, List, Bool, Int, CStr, Enum, File, on_trait_change, Input, Output
+from PYME.recipes.traits import HasTraits, HasStrictTraits, Float, List, Bool, Int, CStr, Enum, File, on_trait_change, Input, Output, Instance
 
 #for some reason traitsui raises SystemExit when called from sphinx on OSX
 #This is due to the framework build problem of anaconda on OSX, and also
@@ -33,15 +33,44 @@
 _legacy_modules = {}
 module_names = {}
 
-def register_module(moduleName):
+def register_module(moduleName, prefix=None):
+    """
+    Register a module so that it is discoverable by the recipe architecture
+
+    Recipe module prefixes are treated slightly differently depending on whether it is a PYME internal
+    recipe, or comes from an external module. For PYME-internal recipe modules, their prefix is the name
+    of the (python) module in which the recipe is defined. For external (plugin) recipe modules, it is
+    the name of the python **package** which contains the recipe module - a plugin may define multiple 
+    recipes in different files, but they will all be accessible using the package prefix. This is a change 
+    from previous behaviour where the most proximal module name was used in plugin derived modules (similar 
+    to internal recipe modules). This change was made to a) decrease the chance of collisions, where plugin
+    modules shadowed exisiting internal recipe modules and b) make module provenance (is this an internal
+    or plugin-derived module) clear to assist debugging.
+
+    If the plugin package name is not sufficiently distinctive, or happens to shadow any of the internal
+    PYME recipe module names, plugin authors have the opportuntiy to specify their own prefix as a second 
+    argument to register_module. If taking this route, the prefix should be an identifier of the 
+    group/individual maintaining the plugin - e.g. baddeleylab. 
+    """
     def c_decorate(cls):
-        py_module = cls.__module__.split('.')[-1]
-        full_module_name = '.'.join([py_module, moduleName])
+        if not prefix:
+            top_level_mod = cls.__module__.split('.')[0]
+            py_module = cls.__module__.split('.')[-1]
+
+            if top_level_mod == 'PYME':
+                prefix_ = py_module
+            else:
+                prefix_ = top_level_mod
+        else:
+            prefix_ = prefix
+
+        full_module_name = '.'.join([prefix_, moduleName])
 
         all_modules[full_module_name] = cls
         _legacy_modules[moduleName] = cls #allow acces by non-hierarchical names for backwards compatibility
 
         module_names[cls] = full_module_name
+        cls._module_name = full_module_name
         return cls
 
     return c_decorate
@@ -60,6 +89,8 @@ def c_decorate(cls):
         _legacy_modules[full_module_name] = cls
         _legacy_modules[moduleName] = cls #allow access by non-hierarchical names for backwards compatibility
 
+        cls._module_name = full_module_name
+
         #module_names[cls] = full_module_name
         return cls
 
@@ -70,7 +101,7 @@ class MissingInputError(Exception):
     pass
 
 
-class ModuleBase(HasTraits):
+class ModuleBase(HasStrictTraits):
     """
     Recipe modules represent a "functional" processing block, the effects of which depend solely on its
     inputs and parameters. They read a number of named inputs from the recipe namespace and write the
@@ -83,7 +114,13 @@ class ModuleBase(HasTraits):
 
     If you want side effects - e.g. saving something to disk, look at the OutputModule class.
     """
-    _invalidate_parent = True
+    _invalidate_parent = Bool(True)
+    _parent=Instance(object)
+
+    _initial_set = Bool(False)
+    _success = Bool(False)
+    _last_error = Instance(object)
+
 
     def __init__(self, parent=None, invalidate_parent = True, **kwargs):
         self._parent = parent