python-microscopy 25.11.20__cp313-cp313-win_amd64.whl

PYME/Acquire/Protocols/htsms-tile.py

@@ -0,0 +1,68 @@
+
+from PYME.Acquire.protocol import *
+from PYME.Acquire.Utils.pointScanner import CircularPointScanner
+import numpy as np
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class Scanner(CircularPointScanner):
+    def __init__(self, scan_radius_um=100):
+        self.enabled_views = []
+        self.scan_radius_um = scan_radius_um
+    
+    def setup(self):
+        fs = np.array((scope.cam.size_x, scope.cam.size_y))
+        # calculate tile spacing such that there is ~30% overlap.
+        tile_spacing = (1/np.sqrt(2)) * fs * np.array(scope.GetPixelSize())
+        # take the pixel size to be the same or at least similar in both directions
+        pixel_radius = int(self.scan_radius_um / tile_spacing.mean())
+        logger.debug('Circular tiler target radius in units of (overlapped) FOVs: %d' % pixel_radius)
+
+        CircularPointScanner.__init__(self, scope, pixel_radius, tile_spacing, 
+                                            1, 0, False, True, trigger=True, 
+                                            stop_on_complete=True, return_to_start=False)
+        self.on_stop.connect(scope.spoolController.StopSpooling)
+        
+        self.genCoords()
+
+        self.check_focus_lock_ok()
+    
+    def check_focus_lock_ok(self):
+        scope.focus_lock.EnableLock()  # make sure we have the lock on
+        if not scope.focus_lock.LockOK():
+            import time
+            logger.debug('lock not OK, pausing for 10 s')
+            time.sleep(10)
+            logger.debug('starting reacquire sequence')
+            scope.focus_lock.ReacquireLock()
+
+
+scanner = Scanner(scan_radius_um=500)
+
+# T(frame, function, *args) creates a new task
+taskList = [
+    T(-1, scope.state.update, {
+        'Lasers.OBIS405.Power': 1.0,
+        'Lasers.OBIS405.On': True,
+        'Multiview.ActiveViews': [1],
+        'Multiview.ROISize': [256, 256],
+        'Camera.IntegrationTime': 0.02,
+    }),
+    T(-1, scope._stage_leveler.acquire_focus_lock),
+    T(-1, scanner.setup),
+    T(0, scanner.start),
+    T(1, scope.l405.TurnOn),  # ~superstitious, but the obis is a punk sometimes
+    T(maxint, scope.turnAllLasersOff),
+]
+
+#optional - metadata entries
+metaData = [
+    ('Protocol.DataStartsAt', 0)
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, filename=__file__)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 20, 100, metaData, 
+                                        randomise=False, filename=__file__)

PYME/Acquire/Protocols/htsms-two-color.py

@@ -0,0 +1,29 @@
+from PYME.Acquire.protocol import *
+
+# T(when, what, *args) creates a new task. "when" is the frame number, "what" is a function to
+# be called, and *args are any additional arguments.
+taskList = [
+    T(-1, scope.state.update, {
+        'Lasers.MPB560.On': True,
+        'Lasers.MPB560.Power': 550.0,
+        'Lasers.MPB642.On': True,
+        'Lasers.MPB642.Power': 575.0,
+        'Multiview.ActiveViews': [0, 1, 2, 3],
+        'Multiview.ROISize': [256, 256],
+        'Camera.IntegrationTime': 0.00125,
+    }),
+    T(0, scope.focus_lock.DisableLock),
+    T(maxint, scope.turnAllLasersOff),
+    T(maxint, scope.focus_lock.EnableLock)
+]
+
+metaData = [
+    ('Protocol.DataStartsAt', 0),
+]
+
+preflight = []  # no preflight checks
+
+# must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight, filename=__file__)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 1, 800, metaData, preflight, slice_order='triangle',
+                                        require_camera_restart=False, filename=__file__)

PYME/Acquire/Protocols/htsms-widefield.py

@@ -0,0 +1,32 @@
+from PYME.Acquire.protocol import *
+
+# T(when, what, *args) creates a new task. "when" is the frame number, "what" is a function to
+# be called, and *args are any additional arguments.
+taskList = [
+    T(-1, scope.state.update, {
+        'Lasers.OBIS405.On': False,
+        'Lasers.OBIS488.On': False,
+        'Lasers.MPB560.On': True,
+        'Lasers.MPB560.Power': 0,
+        'Lasers.MPB642.On': True,
+        'Lasers.MPB642.Power': 0,
+        'Multiview.ActiveViews': [0, 1, 2, 3],
+        'Multiview.ROISize': [256, 256],
+        'Camera.IntegrationTime': 0.025,
+    }),
+    T(-1, scope.focus_lock.DisableLockAfterAcquiringIfEnabled),
+    # T(maxint, scope.turnAllLasersOff),
+    T(maxint, scope.focus_lock.EnableLock)
+]
+
+metadata = [
+    ('Protocol.DataStartsAt', 0),
+]
+
+preflight = []  # no preflight checks
+
+# must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metadata, preflight, filename=__file__)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 1, 1, metadata, preflight,
+                                        require_camera_restart=True, 
+                                        filename=__file__)

PYME/Acquire/Protocols/paint671.py

@@ -0,0 +1,61 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, SetCameraShutter, False),
+T(-1, scope.joystick.Enable, False),
+#T(-1, SetEMGain,150),
+T(20, SetCameraShutter, True),
+T(20, SetEMGain,scope.cam.DefaultEMGain),
+T(21, scope.l671.TurnOn),
+T(70, MainFrame.pan_spool.OnBAnalyse, None),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.joystick.Enable, True),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 22),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of %d' % scope.cam.DefaultEMGain),
+#C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() > .06', 'Camera integration time may be too short'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)

PYME/Acquire/Protocols/photoconversion.py

@@ -0,0 +1,52 @@
+#!/usr/bin/python
+
+##################
+# standard488.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, SetCameraShutter, False),
+T(-1, scope.dichroic.SetFilter, 'FITC'), #Pre-converted
+T(20, SetCameraShutter, True),
+T(30, MainFrame.pan_spool.OnBAnalyse, None),
+T(100, scope.dichroic.SetFilter, 'DAPI'), #Photoconversion
+T(120, scope.dichroic.SetFilter, 'FITC'), #Pre-conv
+T(170, scope.dichroic.SetFilter, 'TxRed'), #Post-conv
+T(220, scope.dichroic.SetFilter, 'DAPI'), #Conversion
+T(240, scope.dichroic.SetFilter, 'TxRed'), #Conversion
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 21)
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 20, 30, metaData, randomise = False)

PYME/Acquire/Protocols/photoconversion2.py

@@ -0,0 +1,55 @@
+#!/usr/bin/python
+
+##################
+# standard488.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+def alternans(start, period, ncycles, chans):
+    return [T(start + period*n, scope.dichroic.SetFilter, chans[n%2]) for n in range(2*ncycles)]
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, SetCameraShutter, False),
+T(-1, scope.dichroic.SetFilter, 'FITC'), #Pre-converted
+T(20, SetCameraShutter, True),
+T(30, MainFrame.pan_spool.OnBAnalyse, None),
+]
+taskList += alternans(40, 10, 5, ['Cy5', 'TxRed'])
+taskList += [T(140, scope.dichroic.SetFilter, 'DAPI'),] #Photoconversion
+taskList += alternans(250, 10, 5, ['Cy5', 'TxRed'])
+
+print(taskList)
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 21)
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 20, 30, metaData, randomise = False)

PYME/Acquire/Protocols/prebleach488.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, SetCameraShutter, False),
+#T(-1, scope.joystick.Enable, False),
+#T(-1, SetEMGain,150),
+T(20, SetCameraShutter, True),
+#T(20, scope.filterWheel.SetFilterPos, "ND4"),
+T(20, scope.l488.SetPower, .01),
+T(21, scope.l488.TurnOn),
+T(58, scope.l488.TurnOff),
+T(60, SetEMGain,0),
+T(61, scope.l488.TurnOn),
+T(61, scope.l488.SetPower, 1),
+T(200, SetEMGain,scope.cam.DefaultEMGain),
+T(210, MainFrame.pan_spool.OnBAnalyse, None),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.l488.SetPower, .01),
+#T(maxint, scope.joystick.Enable, True),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 201),
+('Protocol.PrebleachFrames', (21, 58)),
+('Protocol.BleachFrames', (61,200)),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of %d' % scope.cam.DefaultEMGain),
+C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() < .06', 'Camera integration time may be too long'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)

PYME/Acquire/Protocols/prebleach490.py

@@ -0,0 +1,69 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, scope.joystick.Enable, False),
+T(-1, SetCameraShutter, False),
+T(20, SetCameraShutter, True),
+#T(-1, SetEMGain,150),
+T(20, scope.filterWheel.SetFilterPos, "ND2"),
+T(21, scope.l490.TurnOn),
+T(58, scope.l490.TurnOff),
+T(60, SetEMGain,0),
+T(61, scope.l490.TurnOn),
+T(61, scope.filterWheel.SetFilterPos, "EMPTY"),
+T(150, SetEMGain,scope.cam.DefaultEMGain),
+T(160, MainFrame.pan_spool.OnBAnalyse, None),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.filterWheel.SetFilterPos, "ND2"),
+T(maxint, scope.joystick.Enable, True),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 151),
+('Protocol.PrebleachFrames', (21, 58)),
+('Protocol.BleachFrames', (61,150)),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of 150'),
+C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() < .06', 'Camera integration time may be too long'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)

PYME/Acquire/Protocols/prebleach561.py

@@ -0,0 +1,72 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+T(-1, SetCameraShutter, False),
+T(-1, scope.joystick.Enable, False),
+#T(-1, SetEMGain,150),
+T(10, scope.l561.SetPower,1),
+T(10, scope.l561.TurnOn),
+T(20, SetCameraShutter, True),
+#T(20, scope.filterWheel.SetFilterPos, "ND4"),
+T(20, scope.lAOM.SetPower, .01),
+T(21, scope.lAOM.TurnOn),
+T(58, scope.lAOM.TurnOff),
+T(60, SetEMGain,0),
+T(61, scope.lAOM.TurnOn),
+T(61, scope.lAOM.SetPower, .25),
+T(200, SetEMGain,scope.cam.DefaultEMGain),
+T(210, MainFrame.pan_spool.OnBAnalyse, None),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.lAOM.SetPower, .01),
+T(maxint, scope.joystick.Enable, True),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 201),
+('Protocol.PrebleachFrames', (21, 58)),
+('Protocol.BleachFrames', (61,200)),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of %d' % scope.cam.DefaultEMGain),
+C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() < .06', 'Camera integration time may be too long'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)

PYME/Acquire/Protocols/prebleach561NeomEos2.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+#T(-1, SetCameraShutter, False),
+T(-1, scope.joystick.Enable, False),
+#T(-1, SetEMGain,150),
+#T(20, SetCameraShutter, True),
+T(20, scope.filterWheel.SetFilterPos, "ND4"),
+T(21, scope.l561.TurnOn),
+T(58, scope.l561.TurnOff),
+#T(60, SetEMGain,0),
+T(61, scope.l561.TurnOn),
+T(61, scope.filterWheel.SetFilterPos, "EMPTY"),
+#T(200, SetEMGain,scope.cam.DefaultEMGain),
+T(210, MainFrame.pan_spool.OnBAnalyse, None),
+T(210, scope.l405.TurnOn),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.filterWheel.SetFilterPos, "ND4"),
+T(maxint, scope.joystick.Enable, False),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 201),
+('Protocol.PrebleachFrames', (21, 58)),
+('Protocol.BleachFrames', (61,210)),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+#C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of %d' % scope.cam.DefaultEMGain),
+#C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() < .06', 'Camera integration time may be too long'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)

PYME/Acquire/Protocols/prebleach561NeomEos2ND1.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+##################
+# prebleach671.py
+#
+# Copyright David Baddeley, 2009
+# d.baddeley@auckland.ac.nz
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+
+#import all the stuff to make this work
+from PYME.Acquire.protocol import *
+import numpy
+
+#define a list of tasks, where T(when, what, *args) creates a new task
+#when is the frame number, what is a function to be called, and *args are any
+#additional arguments
+taskList = [
+T(-1, scope.turnAllLasersOff),
+#T(-1, SetCameraShutter, False),
+T(-1, scope.joystick.Enable, False),
+#T(-1, SetEMGain,150),
+#T(20, SetCameraShutter, True),
+T(20, scope.filterWheel.SetFilterPos, "ND4"),
+T(21, scope.l561.TurnOn),
+T(58, scope.l561.TurnOff),
+#T(60, SetEMGain,0),
+T(61, scope.l561.TurnOn),
+T(61, scope.filterWheel.SetFilterPos, "ND1"),
+#T(200, SetEMGain,scope.cam.DefaultEMGain),
+T(210, MainFrame.pan_spool.OnBAnalyse, None),
+T(210, scope.l405.TurnOn),
+T(maxint, scope.turnAllLasersOff),
+T(maxint, scope.filterWheel.SetFilterPos, "ND4"),
+T(maxint, scope.joystick.Enable, False),
+]
+
+#optional - metadata entries
+metaData = [
+('Protocol.DarkFrameRange', (0, 20)),
+('Protocol.DataStartsAt', 201),
+('Protocol.PrebleachFrames', (21, 58)),
+('Protocol.BleachFrames', (61,210)),
+]
+
+#optional - pre-flight check
+#a list of checks which should be performed prior to launching the protocol
+#syntax: C(expression to evaluate (quoted, should have boolean return), message to display on failure),
+preflight = [
+#C('scope.cam.GetEMGain() == scope.cam.DefaultEMGain', 'Was expecting an intial e.m. gain of %d' % scope.cam.DefaultEMGain),
+#C('scope.cam.GetROIX1() > 1', 'Looks like no ROI has been set'),
+C('scope.cam.GetIntegTime() < .06', 'Camera integration time may be too long'),
+]
+
+#must be defined for protocol to be discovered
+PROTOCOL = TaskListProtocol(taskList, metaData, preflight)
+PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 101, 100, metaData, preflight, randomise = False)