Modified for running in Linux and New stage driver #1045
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… communicate via serial to the FTDI chip in Linux. Minor change to loading Photometrics camera.
…n a bug where stopping or starting an acquisition moves the F stage.
…n DAQ, changes should be kept local, however a solution for stage directions should be made.
SJShep
changed the title
AdvancedImagingUTSW
requested review from
annie-xd-wang and
AdvancedImagingUTSW
| @@ -266,26 +266,19 @@ def set_table(self): | |||
| y_stop = float(self.variables["y_end"].get()) | |||
| y_tiles = int(self.variables["y_tiles"].get()) | |||
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| # NOTE: Removed shifting by the origin becuase, it was not clear how to set the origin. | |||
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We should discuss this. I'm hesitant to make the change immediately, but we can consider a better way to communicate the origin.
| @@ -511,8 +511,18 @@ def load_stages( | |||
| exception=TLFTDICommunicationError, | |||
| ) | |||
| ) | |||
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| elif stage_type == "KST101": | |||
| elif stage_type == "KINESIS" and platform.system() == "Linux": | |||
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This is now obsolete with the latest PR.
| @@ -705,7 +711,10 @@ def start_stage( | |||
| from navigate.model.devices.stages.tl_kcube_inertial import TLKIMStage | |||
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| return TLKIMStage(microscope_name, device_connection, configuration, id) | |||
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| elif device_type == "KINESIS": | |||
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This device should also be added to the configuration wizard.
| # camera_names = Camera.get_available_camera_names() | ||
| camera_to_open = Camera.select_camera(camera_connection) | ||
| camera_names = Camera.get_available_camera_names() | ||
| camera_to_open = Camera.select_camera(camera_names[0]) |
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Does this assume only one camera?
| @@ -172,12 +172,14 @@ def set_external_trigger(self, external_trigger=None) -> None: | |||
| self.analog_output_tasks[ | |||
| board_name | |||
| ].triggers.start_trigger.cfg_dig_edge_start_trig(trigger_source) | |||
| try: | |||
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If it was throwing an error, but handled with a try/except statement, why did you have to remove it?
| @@ -988,10 +988,10 @@ def pre_signal_func(self): | |||
| self.z_stack_distance = abs( | |||
| self.start_z_position - float(microscope_state["end_position"]) | |||
| ) | |||
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| # NOTE: added a quick fix for the focus stage moving in a negative direction during z-stack acquisitions. Somehow a negative step needs to be allowed. Flipping the axes direction did not have the desired outcome. | |||
| self.start_focus = float(microscope_state["start_focus"]) | |||
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When you set the set z/f start position and z/f end position, it can't automatically sweep in the negative direction? If not, that seems like we should fix the logic immediately after those event calls.
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Made changes for running Navigate in Ubuntu 22.04 and added a stage driver for the KST101 in Linux.
There are also some changes scattered in to the the tiling, stage and NI related functions that are specific to either Linux or our setup. For example, we made some bad changes to hard code the direction of the focus stage. For these changes a long term solution is needed. Another example is in the NI daq code, the register_done_event function throws an error. The changes should be well commented.