Load capture objects from files. Remove YAML database.

openflexure_microscope/plugins/default/autofocus/api.py

@@ -1,4 +1,5 @@
 import numpy as np
+import logging
 
 from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
 from openflexure_microscope.api.utilities import JsonPayload
@@ -19,7 +20,7 @@ class AutofocusAPI(MicroscopeViewPlugin):
         # Figure out the range of z values to use
         dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
 
-        print("Running autofocus...")
+        logging.info("Running autofocus...")
         task = self.microscope.task.start(self.plugin.autofocus, dz)
 
         # return a handle on the autofocus task
@@ -35,7 +36,7 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
         if backlash < 0:
             backlash = None
 
-        print("Running autofocus...")
+        logging.info("Running autofocus...")
         task = self.microscope.task.start(self.plugin.fast_autofocus, dz, backlash=backlash)
 
         # return a handle on the autofocus task

openflexure_microscope/plugins/default/camera_calibration/plugin.py

@@ -14,7 +14,7 @@ class RecalibrateAPIView(MicroscopeViewPlugin):
         
         # TODO: Figure out the range of z values to use
 
-        print("Starting microscope recalibration...")
+        logging.info("Starting microscope recalibration...")
         task = self.microscope.task.start(self.plugin.recalibrate)
 
         # Return a handle on the autofocus task

openflexure_microscope/plugins/default/scan/api.py

@@ -2,7 +2,7 @@ from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
 from openflexure_microscope.api.utilities import JsonPayload
 
 from flask import request, jsonify, abort
-
+import logging
 
 class TileScanAPI(MicroscopeViewPlugin):
     def post(self):
@@ -34,7 +34,7 @@ class TileScanAPI(MicroscopeViewPlugin):
         metadata = payload.param('metadata', default={}, convert=dict)
         tags = payload.param('tags', default=[], convert=list)
 
-        print("Running tile scan...")
+        logging.info("Running tile scan...")
         task = self.microscope.task.start(
             self.plugin.tile,
             basename=filename,

openflexure_microscope/plugins/loader.py

@@ -67,8 +67,6 @@ def check_module(module_path):
 def name_from_module(plugin_path):
     path_array = plugin_path.split('.')
 
-    print(path_array)
-
     # Truncate namespace of default plugins
     if path_array[0:2] == ['openflexure_microscope', 'plugins']:
         path_array = path_array[2:]
@@ -129,7 +127,7 @@ class PluginMount(object):
     def __init__(self, parent):
         self.parent = parent
         self.plugins = []
-        print("Creating plugin mount")
+        logging.info("Creating plugin mount")
 
     @property
     def state(self):