Added camera parameters to localization and new speed-optimized staple extension.

picasso/design_sequences.py

@@ -190,4 +190,10 @@
     ["P8", "TTATGTTAATG"],
     ["P9", "TTAATTAGGAT"],
     ["P10", "TTATAATGGAT"],
+    ["5xR1", "TTTCCTCCTCCTCCTCCTCCT"],
+    ["5xR2", "AAACCACCACCACCACCACCA"],
+    ["7xR3", "TCCTCTCTCTCTCTCTCTCTC"],
+    ["7xR4", "CAACACACACACACACACACA"],
+    ["5xR5", "CCCTTCTTCTTCTTCTTCTTC"],
+    ["5xR6", "AAAACAACAACAACAACAACAA"]
 ]

picasso/gui/average.py

@@ -20,7 +20,7 @@
 import scipy
 from PyQt5 import QtCore, QtGui, QtWidgets
 
-from .. import io, lib, render
+from .. import io, lib, render, __version__
 
 
 @numba.jit(nopython=True, nogil=True)
@@ -336,7 +336,7 @@ def update_image(self, *args):
 class Window(QtWidgets.QMainWindow):
     def __init__(self):
         super().__init__()
-        self.setWindowTitle("Picasso: Average")
+        self.setWindowTitle(f"Picasso v{__version__}: Average")
         self.resize(512, 512)
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "average.ico")

picasso/gui/average3.py

@@ -20,7 +20,7 @@
 
 from PyQt5 import QtCore, QtGui, QtWidgets
 
-from .. import io, lib, render
+from .. import io, lib, render, __version__
 
 from numpy.lib.recfunctions import stack_arrays
 
@@ -187,7 +187,7 @@ def add_entry(self, path):
 class Window(QtWidgets.QMainWindow):
     def __init__(self):
         super().__init__()
-        self.setWindowTitle("Picasso: Average3")
+        self.setWindowTitle(f"Picasso v{__version__}: Average3")
         self.resize(1024, 512)
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "average.ico")

picasso/gui/design.py

@@ -21,7 +21,7 @@
 
 from .. import io as _io
 from .. import design, design_sequences
-from .. import lib
+from .. import lib, __version__
 
 BASE_SEQUENCES = design_sequences.base_sequences
 PAINT_SEQUENCES = design_sequences.paint_sequences
@@ -1420,7 +1420,7 @@ def foldingScheme(self):
 class MainWindow(QtWidgets.QWidget):
     def __init__(self):
         super(MainWindow, self).__init__()
-        self.setWindowTitle("Picasso: Design")
+        self.setWindowTitle(f"Picasso v{__version__}: Design")
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "design.ico")
         icon = QtGui.QIcon(icon_path)

picasso/gui/filter.py

@@ -20,7 +20,7 @@
 from matplotlib.colors import LogNorm
 import numpy as np
 import os.path
-from .. import io, lib
+from .. import io, lib, __version__
 
 plt.style.use("ggplot")
 
@@ -292,7 +292,7 @@ class Window(QtWidgets.QMainWindow):
     def __init__(self):
         super().__init__()
         # Init GUI
-        self.setWindowTitle("Picasso: Filter")
+        self.setWindowTitle(f"Picasso v{__version__}: Filter")
         self.resize(1100, 750)
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "filter.ico")

picasso/gui/localize.py

@@ -17,7 +17,7 @@
 import numpy as np
 import traceback
 import importlib, pkgutil
-from .. import io, localize, gausslq, gaussmle, zfit, lib, CONFIG, avgroi
+from .. import io, localize, gausslq, gaussmle, zfit, lib, CONFIG, avgroi, __version__
 from collections import UserDict
 
 try:
@@ -1046,7 +1046,7 @@ class Window(QtWidgets.QMainWindow):
     def __init__(self):
         super().__init__()
         # Init GUI
-        self.setWindowTitle("Picasso: Localize")
+        self.setWindowTitle(f"Picasso v{__version__}: Localize")
 
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "localize.ico")
@@ -1797,8 +1797,7 @@ def save_locs(self, path):
                 "Z Calibration Path"
             ] = self.parameters_dialog.z_calibration_path
             localize_info["Z Calibration"] = self.parameters_dialog.z_calibration
-        info = self.info + [localize_info]
-
+        info = self.info + [localize_info | self.camera_info]
         if self.parameters_dialog.calib_astig_checkbox.isChecked():
             print("Correcting astigmatism...")
 

picasso/gui/nanotron.py

@@ -34,7 +34,7 @@
 from PyQt5 import QtCore, QtGui, QtWidgets
 from PyQt5.QtGui import QIcon
 
-from .. import io, lib, render, nanotron
+from .. import io, lib, render, nanotron, __version__
 
 DEFAULT_MODEL_PATH = _ospath.join(os.sep, "picasso", "model", "default_model.sav")
 default_model = False
@@ -890,7 +890,7 @@ def update_image(self, *args):
 class Window(QtWidgets.QMainWindow):
     def __init__(self, parent=None):
         super().__init__(parent)
-        self.setWindowTitle("Picasso: nanoTRON")
+        self.setWindowTitle(f"Picasso v{__version__}: nanoTRON")
         self.resize(768, 512)
         this_directory = os.path.dirname(os.path.realpath(__file__))
         self.icon_path = os.path.join(this_directory, "icons", "nanotron.ico")

picasso/gui/render.py

@@ -37,7 +37,7 @@
 
 import colorsys
 
-from .. import imageprocess, io, lib, postprocess, render, clusterer
+from .. import imageprocess, io, lib, postprocess, render, clusterer, __version__
 from .rotation import RotationWindow
 
 # PyImarisWrite works on windows only
@@ -10554,7 +10554,7 @@ def initUI(self, plugins_loaded):
         """
 
         # general
-        self.setWindowTitle("Picasso: Render")
+        self.setWindowTitle(f"Picasso v{__version__}: Render")
         this_directory = os.path.dirname(os.path.realpath(__file__))
         icon_path = os.path.join(this_directory, "icons", "render.ico")
         icon = QtGui.QIcon(icon_path)
@@ -12049,7 +12049,7 @@ def remove_locs(self):
         for dialog in self.dialogs:
             dialog.close()
         self.menu_bar.clear() #otherwise the menu bar is doubled
-        self.setWindowTitle("Picasso: Render")
+        self.setWindowTitle(f"Picasso v{__version__}: Render")
         self.initUI(plugins_loaded=True)
 
     def rot_win(self):

picasso/gui/simulate.py

@@ -32,7 +32,7 @@
 import os.path as _ospath
 
 from .. import io as _io
-from .. import lib, simulate
+from .. import lib, simulate, __version__
 
 
 def fitFuncBg(x, a, b):
@@ -116,7 +116,7 @@ def fitFuncStd(x, a, b, c):
 class Window(QtWidgets.QMainWindow):
     def __init__(self):
         super().__init__()
-        self.setWindowTitle("Picasso: Simulate")
+        self.setWindowTitle(f"Picasso v{__version__}: Simulate")
         self.setSizePolicy(
             QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding
         )