Squashed commit of the following:

commit c9de425
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 19:12:29 2020 +1000

    Update dependencies in setup.cfg

    Bumped blacs, labscript and labscript_utils versions to `>=3.0.0`

commit d43ced1
Merge: 3863607 1988032
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 22:48:26 2020 -0400

    Merge pull request #58 from philipstarkey/fix-h5py-file-mode

    Fix h5py deprecation warnings

commit 1988032
Author: philipstarkey <[email protected]>
Date:   Thu Jun 25 10:48:10 2020 +1000

    Fix h5py deprecation warnings

    Addresses labscript-suite/labscript-utils#47 for this module

commit 3863607
Merge: 88eeefe cdd34f8
Author: Phil Starkey <[email protected]>
Date:   Wed Jun 24 10:51:04 2020 +1000

    Merge pull request #54 from rpanderson/dummy_pseudoclock_updates

    Save clock instructions and add runviewer parser for DummyPseudoclock

commit 88eeefe
Merge: 55b1bd8 84eb889
Author: Phil Starkey <[email protected]>
Date:   Wed Jun 24 10:50:09 2020 +1000

    Merge pull request #42 from JQIamo/SpinnakerCamera

    Added SpinnakerCamera

commit cdd34f8
Author: philipstarkey <[email protected]>
Date:   Tue Jun 23 18:34:28 2020 +1000

    Implemented review changes

commit d2e5679
Author: Russell Anderson <[email protected]>
Date:   Fri Jun 12 18:47:25 2020 +1000

    Save clock instructions (mock PineBlaster) and add runviewer_parser

commit 84eb889
Author: philipstarkey <[email protected]>
Date:   Tue Jun 23 12:49:00 2020 +1000

    Implemented review changes

commit 55b1bd8
Merge: bb9f6f5 d5fca30
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 18:07:08 2020 +1000

    Merge pull request #57 from philipstarkey/master

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit d5fca30
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 18:33:55 2020 +1000

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit bb9f6f5
Merge: 0f1cacd 091110b
Author: Russell Anderson <[email protected]>
Date:   Fri Jun 19 17:57:15 2020 +1000

    Merge pull request #56 from philipstarkey/master

    Empty sphinx project following our template

commit 091110b
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 17:42:46 2020 +1000

    Empty sphinx project following our template

commit 0f1cacd
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 16:39:08 2020 +1000

    Added missing devices to README.md

commit 5347098
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 11:38:03 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit bd2505e
Author: DSB <[email protected]>
Date:   Mon May 4 14:27:03 2020 -0400

    SpinnakerCamera

    Adding a camera interface that uses FLIR's newer PySpin/Spinnaker API.

    DSB

Co-authored-by: chrisjbillington <[email protected]>
Co-authored-by: Russell Anderson <[email protected]>

Author: 3 people

docs/source/conf.py

@@ -133,8 +133,10 @@
 
 # whether to use stable or latest version
 labscript_suite_doc_version = os.environ.get('READTHEDOCS_VERSION', 'latest')
-if labscript_suite_doc_version not in ['stable', 'latest']:
+if '.' in labscript_suite_doc_version:
     labscript_suite_doc_version = 'stable'
+elif labscript_suite_doc_version not in ['stable', 'latest']:
+    labscript_suite_doc_version = 'latest'
 
 # add intersphinx references for each component
 for ls_prog in labscript_suite_programs:
@@ -205,7 +207,7 @@ def setup(app):
     app.add_config_value('m2r_anonymous_references', False, 'env')
     app.add_config_value('m2r_disable_inline_math', False, 'env')
     app.add_directive('mdinclude', MdInclude)
-    app.add_stylesheet('custom.css')
+    app.add_css_file('custom.css')
 
     # generate the components.rst file dynamically so it points to stable/latest
     # of subprojects correctly

labscript_devices/AlazarTechBoard.py

@@ -316,7 +316,7 @@ def init(self):
     def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
         self.h5file = h5file  # We'll need this in transition_to_manual
         self.device_name = device_name
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             print("\nUsing "+h5file)
             self.atsparam = atsparam = labscript_utils.properties.get(
                 hdf5_file, device_name, 'device_properties')
@@ -379,7 +379,7 @@ def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
 
         # Store the actual acquisition rate back as an attribute.
         # Again, this should be done as an ACQUISITIONS table entry, but not today
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r+') as hdf5_file:
             hdf5_file['devices'][device_name].attrs.create(
                 'acquisition_rate', actual_acquisition_rate, dtype='int32')
 
@@ -585,7 +585,7 @@ def transition_to_manual(self):
         # Waits on the acquisition thread, and manages the lock
         self.wait_acquisition_complete()
         # Write data to HDF5 file
-        with h5py.File(self.h5file) as hdf5_file:
+        with h5py.File(self.h5file, 'r+') as hdf5_file:
             grp = hdf5_file.create_group('/data/traces/'+self.device_name)
             if self.channels & ats.CHANNEL_A:
                 dsetA = grp.create_dataset(

labscript_devices/DummyPseudoclock/labscript_devices.py

@@ -15,24 +15,109 @@
 # and labscript. The device is a PseudoclockDevice, and can be the sole device
 # in a connection table or experiment.
 
-import labscript_utils.h5_lock
-import h5py
-from labscript import PseudoclockDevice, Pseudoclock, ClockLine
+from labscript import PseudoclockDevice, Pseudoclock, ClockLine, config, LabscriptError
+import numpy as np
+
+class _DummyPseudoclock(Pseudoclock):    
+    def add_device(self, device):
+        if isinstance(device, ClockLine):
+            # only allow one child
+            if self.child_devices:
+                raise LabscriptError('The pseudoclock of the DummyPseudoclock %s only supports 1 clockline, which is automatically created. Please use the clockline located at %s.clockline'%(self.parent_device.name, self.parent_device.name))
+            Pseudoclock.add_device(self, device)
+        else:
+            raise LabscriptError('You have connected %s to %s (the Pseudoclock of %s), but %s only supports children that are ClockLines. Please connect your device to %s.clockline instead.'%(device.name, self.name, self.parent_device.name, self.name, self.parent_device.name))
 
 
 class DummyPseudoclock(PseudoclockDevice):
 
     description = 'Dummy pseudoclock'
-    clock_limit = 1e6
-    clock_resolution = 1e-6
+    clock_limit = 10e6
+    clock_resolution = 25e-9
+    trigger_delay = 350e-9
+    wait_delay = 2.5e-6
+    allowed_children = [_DummyPseudoclock]
+    max_instructions = 1e5
 
-    def __init__(self, name='dummy_pseudoclock', BLACS_connection='dummy_connection', **kwargs):
+    def __init__(
+        self, name='dummy_pseudoclock', BLACS_connection='dummy_connection', **kwargs
+    ):
         self.BLACS_connection = BLACS_connection
         PseudoclockDevice.__init__(self, name, None, None, **kwargs)
-        self.pseudoclock = Pseudoclock(self.name + '_pseudoclock', self, 'pseudoclock')
-        self.clockline = ClockLine(name='clockline', pseudoclock=self.pseudoclock, connection='dummy')
+        self._pseudoclock = _DummyPseudoclock(
+            name=f'{name}_pseudoclock',
+            pseudoclock_device=self,
+            connection='pseudoclock',
+        )
+        self._clock_line = ClockLine(
+            name=f'{name}_clock_line',
+            pseudoclock=self.pseudoclock,
+            connection='internal',
+        )
+
+    @property
+    def pseudoclock(self):
+        return self._pseudoclock
+
+    @property
+    def clockline(self):
+        return self._clock_line
+
+    def add_device(self, device):
+        if not self.child_devices and isinstance(device, Pseudoclock):
+            PseudoclockDevice.add_device(self, device)            
+        elif isinstance(device, Pseudoclock):
+            raise LabscriptError('The %s %s automatically creates a Pseudoclock because it only supports one. '%(self.description, self.name) +
+                                 'Instead of instantiating your own Pseudoclock object, please use the internal' +
+                                 ' one stored in %s.pseudoclock'%self.name)
+        else:
+            raise LabscriptError('You have connected %s (class %s) to %s, but %s does not support children with that class.'%(device.name, device.__class__, self.name, self.name))
 
     def generate_code(self, hdf5_file):
         PseudoclockDevice.generate_code(self, hdf5_file)
         group = self.init_device_group(hdf5_file)
-        self.set_property('stop_time', self.stop_time, location='device_properties')
+
+        # Compress clock instructions with the same period
+        # This will halve the number of instructions roughly,
+        # since the DummyPseudoclock does not have a 'slow clock'
+        reduced_instructions = []
+        for instruction in self.pseudoclock.clock:
+            if instruction == 'WAIT':
+                # The following period and reps indicates a wait instruction
+                reduced_instructions.append({'period': 0, 'reps': 1})
+                continue
+            reps = instruction['reps']
+            # period is in quantised units:
+            period = int(round(instruction['step'] / self.clock_resolution))
+            if reduced_instructions and reduced_instructions[-1]['period'] == period:
+                reduced_instructions[-1]['reps'] += reps
+            else:
+                reduced_instructions.append({'period': period, 'reps': reps})
+        # The following period and reps indicates a stop instruction:
+        reduced_instructions.append({'period': 0, 'reps': 0})
+        if len(reduced_instructions) > self.max_instructions:
+            raise LabscriptError(
+                "%s %s has too many instructions. It has %d and can only support %d"
+                % (
+                    self.description,
+                    self.name,
+                    len(reduced_instructions),
+                    self.max_instructions,
+                )
+            )
+        # Store these instructions to the h5 file:
+        dtypes = [('period', int), ('reps', int)]
+        pulse_program = np.zeros(len(reduced_instructions), dtype=dtypes)
+        for i, instruction in enumerate(reduced_instructions):
+            pulse_program[i]['period'] = instruction['period']
+            pulse_program[i]['reps'] = instruction['reps']
+        group.create_dataset(
+            'PULSE_PROGRAM', compression=config.compression, data=pulse_program
+        )
+        # TODO: is this needed, the PulseBlasters don't save it...
+        self.set_property(
+            'is_master_pseudoclock',
+            self.is_master_pseudoclock,
+            location='device_properties',
+        )
+        self.set_property('stop_time', self.stop_time, location='device_properties')

labscript_devices/DummyPseudoclock/register_classes.py

@@ -12,8 +12,12 @@
 #####################################################################
 import labscript_devices
 
+labscript_device_name = 'DummyPseudoclock'
+blacs_tab = 'labscript_devices.DummyPseudoclock.blacs_tabs.DummyPseudoclockTab'
+parser = 'labscript_devices.DummyPseudoclock.runviewer_parsers.DummyPseudoclockParser'
+
 labscript_devices.register_classes(
-    'DummyPseudoclock',
-    BLACS_tab='labscript_devices.DummyPseudoclock.blacs_tabs.DummyPseudoclockTab',
-    runviewer_parser=None, #TODO make a runviwer parser for Dummy pseudoclock!
+    labscript_device_name=labscript_device_name,
+    BLACS_tab=blacs_tab,
+    runviewer_parser=parser,
 )

labscript_devices/DummyPseudoclock/runviewer_parsers.py

@@ -0,0 +1,64 @@
+import labscript_utils.h5_lock  # noqa: F401
+import h5py
+import numpy as np
+
+
+class DummyPseudoclockParser(object):
+    clock_resolution = 25e-9
+    trigger_delay = 350e-9
+    wait_delay = 2.5e-6
+
+    def __init__(self, path, device):
+        self.path = path
+        self.name = device.name
+        self.device = device
+
+    def get_traces(self, add_trace, clock=None):
+        if clock is not None:
+            times, clock_value = clock[0], clock[1]
+            clock_indices = np.where((clock_value[1:] - clock_value[:-1]) == 1)[0] + 1
+            # If initial clock value is 1, then this counts as a rising edge
+            # (clock should be 0 before experiment) but this is not picked up
+            # by the above code. So we insert it!
+            if clock_value[0] == 1:
+                clock_indices = np.insert(clock_indices, 0, 0)
+            clock_ticks = times[clock_indices]
+
+        # get the pulse program
+        with h5py.File(self.path, 'r') as f:
+            pulse_program = f[f'devices/{self.name}/PULSE_PROGRAM'][:]
+
+        time = []
+        states = []
+        trigger_index = 0
+        t = 0 if clock is None else clock_ticks[trigger_index] + self.trigger_delay
+        trigger_index += 1
+
+        clock_factor = self.clock_resolution / 2.0
+
+        for row in pulse_program:
+            if row['period'] == 0:
+                # special case
+                if row['reps'] == 1:  # WAIT
+                    if clock is not None:
+                        t = clock_ticks[trigger_index] + self.trigger_delay
+                        trigger_index += 1
+                    else:
+                        t += self.wait_delay
+            else:
+                for i in range(row['reps']):
+                    for j in range(1, -1, -1):
+                        time.append(t)
+                        states.append(j)
+                        t += row['period'] * clock_factor
+
+        clock = (np.array(time), np.array(states))
+
+        clocklines_and_triggers = {}
+        for pseudoclock_name, pseudoclock in self.device.child_list.items():
+            for clock_line_name, clock_line in pseudoclock.child_list.items():
+                if clock_line.parent_port == 'internal':
+                    clocklines_and_triggers[clock_line_name] = clock
+                    add_trace(clock_line_name, clock, self.name, clock_line.parent_port)
+
+        return clocklines_and_triggers

labscript_devices/FunctionRunner/labscript_devices.py

@@ -50,7 +50,7 @@ def func(shot_context, t, ...):
         recommended place to do it is within the group 'data/<device_name>', for
         example:
 
-            with h5py.File(self.h5_file) as f:
+            with h5py.File(self.h5_file, 'r+') as f:
                 data_group = f['data'].create_group(self.device_name)
                 # save datasets/attributes within this group
 

labscript_devices/IMAQdxCamera/blacs_workers.py

@@ -429,7 +429,7 @@ def transition_to_manual(self):
 
         print(f"Saving {len(self.images)}/{len(self.exposures)} images.")
 
-        with h5py.File(self.h5_filepath) as f:
+        with h5py.File(self.h5_filepath, 'r+') as f:
             # Use orientation for image path, device_name if orientation unspecified
             if self.orientation is not None:
                 image_path = 'images/' + self.orientation

labscript_devices/LightCrafterDMD.py

@@ -317,7 +317,7 @@ def program_manual(self, values):
         return {}
 
     def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             if 'IMAGE_TABLE' in group:
                 table_data = group['IMAGE_TABLE'][:]

labscript_devices/NovaTechDDS9M.py

@@ -457,7 +457,7 @@ def transition_to_buffered(self,device_name,h5file,initial_values,fresh):
         self.final_values = {}
         static_data = None
         table_data = None
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             # If there are values to set the unbuffered outputs to, set them now:
             if 'STATIC_DATA' in group:

labscript_devices/PhaseMatrixQuickSyn.py

@@ -333,7 +333,7 @@ def transition_to_buffered(self,device_name,h5file,initial_values,fresh):
         self.initial_values = initial_values
         # Store the final values to for use during transition_to_static:
         self.final_values = {}
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             # If there are values to set the unbuffered outputs to, set them now:
             if 'STATIC_DATA' in group: