Dax dev - Zarr Implementation/Created dummy model/Updated paths for p…

…ackaging (#113)

* #81 Error handling now in place

* Wired up moving frames to zarr

Co-Authored-By: Dax Collison <[email protected]>

* Thread name printing with exception

Co-Authored-By: Dax Collison <[email protected]>

* Comment

Co-Authored-By: Dax Collison <[email protected]>

* Moving along on zarr saving

Co-Authored-By: Dax Collison <[email protected]>

* Update aslm_image_writer.py

Co-Authored-By: Dax Collison <[email protected]>

* Boolean flags based on stack cycle mode

Co-Authored-By: Dax Collison <[email protected]>

* Zarr array is now updated with data

Still very early and is not ready to be pulled

Co-Authored-By: Dax Collison <[email protected]>

* Removing for loops to add image to zarr array

* Updating copy to zarr function

* Updating test for image writer

* Basic Setup.py

* Synthetic Hardware Test now compatible with structure

* Basic Setup.py

* Revert "Basic Setup.py"

This reverts commit 53385f4.

* Fixing path issues for model tests to run

* Created dummy model

I put the dummy model in the aslm package bc I was having import errors trying to import modules from the test folder.

* Updated paths to absolute

Can now run aslm --sh in command line after installing and will run program

* Adding zarr for github tests

* Update dummy model and apply to tests

* Removing init from test classes

* This will now pass

Aslm Analysis test needs to be addressed as its calling an entropy funciton that doesn't exist where it maybe is supposed to

Co-authored-by: AdvancedImagingUTSW <[email protected]>

requirements.txt

@@ -17,3 +17,4 @@ tensorflow==2.8.0
 cupy-cuda112==10.2.0
 protobuf==3.20.*
 zarr==2.11.3
+

setup.py

@@ -11,3 +11,4 @@
      },
      include_package_data=True,
  ) 
+

src/aslm/controller/aslm_controller.py

@@ -41,30 +41,30 @@
 
 # Local View Imports
 from tkinter import filedialog
-from view.main_application_window import Main_App as view
-from view.remote_focus_popup import remote_popup
-from view.autofocus_setting_popup import autofocus_popup
+from aslm.view.main_application_window import Main_App as view
+from aslm.view.remote_focus_popup import remote_popup
+from aslm.view.autofocus_setting_popup import autofocus_popup
 
 # Local Sub-Controller Imports
-from controller.sub_controllers.stage_gui_controller import Stage_GUI_Controller
-from controller.sub_controllers.acquire_bar_controller import Acquire_Bar_Controller
-from controller.sub_controllers.channels_tab_controller import Channels_Tab_Controller
-from controller.sub_controllers.camera_view_controller import Camera_View_Controller
-from controller.sub_controllers.camera_setting_controller import Camera_Setting_Controller
-from controller.aslm_configuration_controller import ASLM_Configuration_Controller
-from controller.sub_controllers.waveform_tab_controller import Waveform_Tab_Controller
-from controller.sub_controllers.etl_popup_controller import Etl_Popup_Controller
-from controller.sub_controllers.autofocus_popup_controller import Autofocus_Popup_Controller
-from controller.aslm_controller_functions import *
-from controller.thread_pool import SynchronizedThreadPool
+from aslm.controller.sub_controllers.stage_gui_controller import Stage_GUI_Controller
+from aslm.controller.sub_controllers.acquire_bar_controller import Acquire_Bar_Controller
+from aslm.controller.sub_controllers.channels_tab_controller import Channels_Tab_Controller
+from aslm.controller.sub_controllers.camera_view_controller import Camera_View_Controller
+from aslm.controller.sub_controllers.camera_setting_controller import Camera_Setting_Controller
+from aslm.controller.aslm_configuration_controller import ASLM_Configuration_Controller
+from aslm.controller.sub_controllers.waveform_tab_controller import Waveform_Tab_Controller
+from aslm.controller.sub_controllers.etl_popup_controller import Etl_Popup_Controller
+from aslm.controller.sub_controllers.autofocus_popup_controller import Autofocus_Popup_Controller
+from aslm.controller.aslm_controller_functions import *
+from aslm.controller.thread_pool import SynchronizedThreadPool
 
 # Local Model Imports
-from model.aslm_model import Model
-from model.aslm_model_config import Session as session
-from model.concurrency.concurrency_tools import ObjectInSubprocess, SharedNDArray
+from aslm.model.aslm_model import Model
+from aslm.model.aslm_model_config import Session as session
+from aslm.model.concurrency.concurrency_tools import ObjectInSubprocess, SharedNDArray
 
 # debug
-from controller.aslm_debug import Debug_Module
+from aslm.controller.aslm_debug import Debug_Module
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/acquire_bar_controller.py

@@ -35,8 +35,8 @@
 POSSIBILITY OF SUCH DAMAGE.
 """
 import sys
-from controller.sub_controllers.gui_controller import GUI_Controller
-from view.main_window_content.acquire_bar_frame.acquire_popup import Acquire_PopUp as acquire_popup
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.view.main_window_content.acquire_bar_frame.acquire_popup import Acquire_PopUp as acquire_popup
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/autofocus_popup_controller.py

@@ -32,8 +32,8 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 """
-from controller.sub_controllers.gui_controller import GUI_Controller
-from controller.aslm_controller_functions import combine_funcs
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.aslm_controller_functions import combine_funcs
 import time
 
 import logging

src/aslm/controller/sub_controllers/camera_setting_controller.py

@@ -32,7 +32,7 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 """
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/camera_view_controller.py

@@ -43,7 +43,7 @@
 import numpy as np
 
 # Local Imports
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 
 # Logger Setup
 p = __name__.split(".")[0]

src/aslm/controller/sub_controllers/channel_setting_controller.py

@@ -32,8 +32,8 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 """
-from controller.sub_controllers.widget_functions import validate_wrapper
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.widget_functions import validate_wrapper
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 import logging
 from pathlib import Path
 # Logger Setup

src/aslm/controller/sub_controllers/channels_tab_controller.py

@@ -33,10 +33,10 @@
 POSSIBILITY OF SUCH DAMAGE.
 """
 import numpy as np
-from controller.sub_controllers.widget_functions import validate_wrapper
-from controller.sub_controllers.gui_controller import GUI_Controller
-from controller.sub_controllers.channel_setting_controller import Channel_Setting_Controller
-from controller.sub_controllers.multi_position_controller import Multi_Position_Controller
+from aslm.controller.sub_controllers.widget_functions import validate_wrapper
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.channel_setting_controller import Channel_Setting_Controller
+from aslm.controller.sub_controllers.multi_position_controller import Multi_Position_Controller
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/etl_popup_controller.py

@@ -34,9 +34,9 @@
 """
 from tkinter import filedialog
 
-from controller.sub_controllers.widget_functions import validate_wrapper
-from controller.sub_controllers.gui_controller import GUI_Controller
-from controller.aslm_controller_functions import save_yaml_file, combine_funcs
+from aslm.controller.sub_controllers.widget_functions import validate_wrapper
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.aslm_controller_functions import save_yaml_file, combine_funcs
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/multi_position_controller.py

@@ -37,7 +37,7 @@
 import pandas as pd
 from pandastable import TableModel
 
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 
 import logging
 from pathlib import Path

src/aslm/controller/sub_controllers/stage_gui_controller.py

@@ -32,8 +32,8 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 """
-from controller.sub_controllers.widget_functions import validate_wrapper
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.widget_functions import validate_wrapper
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 import logging
 from pathlib import Path
 # Logger Setup

src/aslm/controller/sub_controllers/waveform_tab_controller.py

@@ -32,7 +32,7 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 """
-from controller.sub_controllers.gui_controller import GUI_Controller
+from aslm.controller.sub_controllers.gui_controller import GUI_Controller
 from matplotlib.backends.backend_tkagg import (FigureCanvasTkAgg)
 from matplotlib.figure import Figure
 import logging

src/aslm/log_files/log_functions.py

@@ -1,4 +1,4 @@
-import logging
+import logging.config
 import logging.handlers
 import multiprocessing
 import yaml

src/aslm/log_files/logging.yml

@@ -6,9 +6,9 @@ formatters:
     format: '%(asctime)s - %(name)s - %(levelname)s - %(module)s: %(message)s'
 filters:
   performance_specs:
-    (): ext://log_files.filters.PerformanceFilter
+    (): ext://aslm.log_files.filters.PerformanceFilter
   not_performance:
-    (): ext://log_files.filters.NonPerfFilter
+    (): ext://aslm.log_files.filters.NonPerfFilter
 handlers:
   console:
     class: logging.StreamHandler
@@ -20,21 +20,21 @@ handlers:
     class: logging.FileHandler
     level: INFO
     formatter: base
-    filename: log_files/view_controller_info.log
+    filename: aslm/log_files/view_controller_info.log
     filters: [not_performance]
     mode: w
   vc_debug:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/view_controller_debug.log
+    filename: aslm/log_files/view_controller_debug.log
     filters: [not_performance]
     mode: w
   performance:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/performance.log
+    filename: aslm/log_files/performance.log
     filters: [performance_specs]
     mode: w
 loggers:

src/aslm/log_files/model_logging.yml

@@ -6,9 +6,9 @@ formatters:
     format: '%(asctime)s - %(name)s - %(levelname)s - %(module)s: %(message)s'
 filters:
   performance_specs:
-    (): ext://log_files.filters.PerformanceFilter
+    (): ext://aslm.log_files.filters.PerformanceFilter
   not_performance:
-    (): ext://log_files.filters.NonPerfFilter
+    (): ext://aslm.log_files.filters.NonPerfFilter
 handlers:
   console:
     class: logging.StreamHandler
@@ -20,21 +20,21 @@ handlers:
     class: logging.FileHandler
     level: INFO
     formatter: base
-    filename: log_files/model_info.log
+    filename: aslm/log_files/model_info.log
     filters: [not_performance]
     mode: w
   model_debug:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/model_debug.log
+    filename: aslm/log_files/model_debug.log
     filters: [not_performance]
     mode: w
   model_performance:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/model_performance.log
+    filename: aslm/log_files/model_performance.log
     filters: [performance_specs]
     mode: w
 loggers:

src/aslm/main.py

@@ -47,11 +47,11 @@
 import platform
 import logging
 import logging.config
-from log_files.log_functions import log_setup
+from aslm.log_files.log_functions import log_setup
 import yaml
 
 # Local Imports
-from controller.aslm_controller import ASLM_controller as controller
+from aslm.controller.aslm_controller import ASLM_controller as controller
 
 def main():
     """

src/aslm/model/aslm_analysis.py

@@ -44,7 +44,7 @@
     import tensorflow as tf
 
 # Local Imports
-from .analysis import image_decorrelation as image_decorrelation
+from aslm.model.analysis import image_decorrelation as image_decorrelation
 
 # Logger Setup
 p = __name__.split(".")[0]
@@ -56,7 +56,7 @@ def __init__(self, use_gpu=False, verbose=False):
         self.use_gpu = use_gpu
 
         if use_gpu:
-            from .analysis import flatfield as flatfield
+            from aslm.model.analysis import flatfield as flatfield
 
     def __del__(self):
         pass

src/aslm/model/aslm_debug_model.py

@@ -50,9 +50,9 @@
 
 from multiprocessing import Pool, Lock
 
-from model.aslm_device_startup_functions import start_analysis
-from model.concurrency.concurrency_tools import ObjectInSubprocess
-from model.aslm_analysis import Analysis
+from aslm.model.aslm_device_startup_functions import start_analysis
+from aslm.model.concurrency.concurrency_tools import ObjectInSubprocess
+from aslm.model.aslm_analysis import Analysis
 
 # Logger Setup
 p = __name__.split(".")[0]