Updates to tiling, protocol file save organization, protocol run fixe…

…s, protocol defaults. (#303)

data/example_protocol.tsv

@@ -1,9 +1,9 @@
 LumaViewPro Protocol
-Period	0.1
-Duration	1.2
+Period	20.0
+Duration	48.0
 Labware	96 well microplate
 Name	X	Y	Z	Auto_Focus	Channel	False_Color	Illumination	Gain	Auto_Gain	Exposure
-	46.5	36.999963199999996	7168.49698	1.0	0.0	1.0	100.0	10.0	0.0	100.0
+	46.5	37.0	7168.5	1.0	0.0	1.0	100.0	10.0	0.0	100.0
 	46.5	37.0	7168.5	0.0	1.0	0.0	100.0	10.0	0.0	100.0
 	46.5	37.0	7168.5	0.0	2.0	0.0	100.0	10.0	0.0	100.0
 	55.5	37.0	7168.5	0.0	0.0	1.0	100.0	10.0	0.0	100.0

data/new_default_protocol.tsv

@@ -0,0 +1,5 @@
+LumaViewPro Protocol
+Period	20.0
+Duration	48.0
+Labware	96 well microplate
+Name	X	Y	Z	Auto_Focus	Channel	False_Color	Illumination	Gain	Auto_Gain	Exposure

data/settings.json

@@ -29,7 +29,6 @@
         "z": 4950.0
     },
     "BF": {
-        "save_folder": "./capture",
         "file_root": "BF_",
         "focus": 4950.0,
         "autofocus": false,
@@ -41,7 +40,6 @@
         "acquire": false
     },
     "PC": {
-        "save_folder": "./capture",
         "file_root": "PC_",
         "focus": 4950.0,
         "autofocus": false,
@@ -53,10 +51,9 @@
         "acquire": false
     },
     "EP": {
-        "save_folder": "./capture",
         "file_root": "EP_",
         "focus": 4950.0,
-        "autofocus": true,
+        "autofocus": false,
         "false_color": false,
         "ill": 100.0,
         "gain": 1.0,
@@ -65,7 +62,6 @@
         "acquire": false
     },
     "Blue": {
-        "save_folder": "./capture",
         "file_root": "B_",
         "focus": 4950.0,
         "autofocus": false,
@@ -77,7 +73,6 @@
         "acquire": false
     },
     "Green": {
-        "save_folder": "./capture",
         "file_root": "G_",
         "focus": 4950.0,
         "autofocus": false,
@@ -89,7 +84,6 @@
         "acquire": false
     },
     "Red": {
-        "save_folder": "./capture",
         "file_root": "R_",
         "focus": 4950.0,
         "autofocus": false,
@@ -107,8 +101,8 @@
     },
     "protocol": {
         "period": 20,
-        "duration": 20,
+        "duration": 48,
         "labware": "96 well microplate",
-        "filepath": "./data/example_protocol.tsv"
+        "filepath": "./data/new_default_protocol.tsv"
     }
-}
+}

data/tiling.json

@@ -0,0 +1,49 @@
+{
+  "metadata": {
+    "name": "tiling",
+    "version": 1,
+    "default": "1x1"
+  },
+  "data": {
+    "1x1": {
+      "m": 1,
+      "n": 1
+    },
+    "2x2": {
+      "m": 2,
+      "n": 2
+    },
+    "3x3": {
+      "m": 3,
+      "n": 3
+    },
+    "4x4": {
+      "m": 4,
+      "n": 4
+    },
+    "5x5": {
+      "m": 5,
+      "n": 5
+    },
+    "6x6": {
+      "m": 6,
+      "n": 6
+    },
+    "7x7": {
+      "m": 7,
+      "n": 7
+    },
+    "8x8": {
+      "m": 8,
+      "n": 8
+    },
+    "9x9": {
+      "m": 9,
+      "n": 9
+    },
+    "10x10": {
+      "m": 10,
+      "n": 10
+    }
+  }
+}

labware.py

@@ -90,7 +90,7 @@ def set_indices(self, stitch=1):
 
         if stitch > 1:
             for i in range(stitch):
-                for j in range(stich):
+                for j in range(stitch):
                     if j % 2 == 1:
                         i = self.plate['columns'] - i - 1
                     self.stitch_list.append([i,j])
@@ -137,6 +137,12 @@ def get_well_index(self, x, y):
         return i, j
 
 
+    def get_well_label(self, x, y):
+        well_x, well_y = self.get_well_index(x=x, y=y)
+        letter = chr(ord('A') + well_y)
+        return f'{letter}{well_x + 1}'
+
+
 class PitriDish(LabWare):
     """A class that stores and computes actions for petri dish labware"""
 

lumascope_api.py

@@ -43,6 +43,7 @@
 
 # Import additional libraries
 from lvp_logger import logger
+import pathlib
 import time
 import threading
 import os
@@ -168,6 +169,10 @@ def get_next_save_path(self, path):
 
         """
 
+        # TODO for now converting pathlib.Path's to strings for the algorithm below
+        if issubclass(type(path), pathlib.Path):
+            path = str(path)
+
         # Extract file extension (.tiff) and file_id (00001)
         dot_idx = path.rfind('.') 
         under_idx = path.rfind('_')
@@ -185,7 +190,7 @@ def get_next_save_path(self, path):
 
         return f'{path[:under_idx]}_{new_file_id}.{file_extension}'
 
-    def save_image(self, array, save_folder = './capture', file_root = 'img_', append = 'ms', color = 'BF'):
+    def save_image(self, array, save_folder = './capture', file_root = 'img_', append = 'ms', color = 'BF', tail_id_mode = "increment"):
         """CAMERA FUNCTIONS
         save image (as array) to file
         """
@@ -213,29 +218,52 @@ def save_image(self, array, save_folder = './capture', file_root = 'img_', appen
         # else:
         #     append = ''
 
-        # generate filename and save path string
-        initial_id = '_000001'
-        filename =  file_root + append + initial_id + '.tiff'
-        path = save_folder + '/' + filename
+        if type(save_folder) == str:
+            save_folder = pathlib.Path(save_folder)
 
-        # Obtain next save path if current directory already exists
-        while os.path.exists(path):
-            path = self.get_next_save_path(path)
+        if file_root is None:
+            file_root = ""
+
+        # generate filename and save path string
+        if tail_id_mode == "increment":
+            initial_id = '_000001'
+            filename =  file_root + append + initial_id + '.tiff'
+            path = save_folder / filename
+
+            # Obtain next save path if current directory already exists
+            while os.path.exists(path):
+                path = self.get_next_save_path(path)
+
+        elif tail_id_mode == None:
+            filename =  file_root + append + '.tiff'
+            path = save_folder / filename
+
+        else:
+            raise Exception(f"tail_id_mode: {tail_id_mode} not implemented")
+
 
         try:
-            cv2.imwrite(path, img.astype(np.uint8))
+            cv2.imwrite(str(path), img.astype(np.uint8))
             logger.info(f'[SCOPE API ] Saving Image to {path}')
         except:
             logger.exception("[SCOPE API ] Error: Unable to save. Perhaps save folder does not exist?")
 
-    def save_live_image(self, save_folder = './capture', file_root = 'img_', append = 'ms', color = 'BF'):
+    def save_live_image(
+            self,
+            save_folder = './capture',
+            file_root = 'img_',
+            append = 'ms',
+            color = 'BF',
+            tail_id_mode = "increment"
+        ):
+
         """CAMERA FUNCTIONS
         Grab the current live image and save to file
         """
         array = self.get_image()
         if array is False:
             return 
-        self.save_image(array, save_folder, file_root, append, color)
+        self.save_image(array, save_folder, file_root, append, color, tail_id_mode)
 
     def get_max_width(self):
         """CAMERA FUNCTIONS

lumaviewpro.kv

@@ -1061,13 +1061,12 @@
             Spinner:
                 id: tiling_size_spinner
                 sync_height: True
-                text: 'New'
+                text: ''
                 font_size: '12dp'
                 size_hint_y: None
                 height: '30dp'
                 text_autoupdate: True
-                on_text: root.select_tiling_size()
-                values: '1x1', '2x2', '3x3', '4x4', '5x5', '6x6', '7x7', '8x8', '9x9'
+                values: ''
 
 
         # # Z-stack
@@ -1528,25 +1527,6 @@
             disabled: True
             font_size: '12sp'
 
-    BoxLayout:
-        orientation: 'horizontal'
-        size_hint_y: None
-        height: '30dp'
-        Label:
-            text: 'Field of View'
-            size_hint_x: None
-            width: '120dp'
-			font_size: '12sp'
-        TextInput:
-            id: FOV_id
-            multiline: False
-            padding: ['5dp', (self.height-self.line_height)/2]
-            halign: 'center'
-            # input_filter: 'int'
-            text: 'tbd'
-			disabled: True
-			font_size: '12sp'
-
 	# Frame Size
 	BoxLayout:
 		orientation: 'horizontal'
@@ -1961,34 +1941,6 @@
 					valign: 'middle'
 					text_size: self.size
 
-			BoxLayout:
-				orientation: 'horizontal'
-				size_hint_y: None
-				height: '30dp'
-				spacing: '5dp'
-				FolderChooseBTN:
-					id: folder_btn
-					# size_hint_y: None
-					# height: '30dp'
-					# font_size: '12sp'
-					# text: 'Folder'
-					border: 0, 0, 0, 0
-					background_normal: './data/icons/folder.png' # Press to Select Folder
-					background_down: './data/icons/folder_down.png'
-					size_hint: None, None
-					size: '30dp', '30dp'
-					on_release: self.choose(root.layer)
-				TextInput:
-					id: root_text
-					# size_hint_y: None
-					# height: '30dp'
-					font_size: '12sp'
-					multiline: False
-					text: 'File Root'
-					padding: ['5dp', (self.height-self.line_height)/2]
-					on_text: root.root_text()
-					hint_text: 'Filename Root'
-
 			Label:
 
 <Histogram>: