Merge pull request #388 from jungmannlab/development

RCC error solve, remove tqdm from gui

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.3
+current_version = 0.6.4
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.gitignore

@@ -77,6 +77,9 @@ target/
 # Mac Desktop Service Store
 **/.DS_Store
 
+# vscode settings
+.vscode/
+
 # Jupyter Notebook
 .ipynb_checkpoints
 

changelog.rst

@@ -3,6 +3,10 @@ Changelog
 
 Last change: 26-SEP-2023 MTS
 
+0.6.4
+-----
+- Fix RCC error for Render GUI (one click installer) (remove tqdm from GUI)
+
 0.6.3
 -----
 - Dependencies updated

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.6.3
+AppVersion=0.6.4
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.3"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.4"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.6.3"
+release = "0.6.4"
 
 # -- General configuration ---------------------------------------------------
 

picasso/__init__.py

@@ -8,7 +8,7 @@
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.6.3"
+__version__ = "0.6.4"
 
 _this_file = _ospath.abspath(__file__)
 _this_dir = _ospath.dirname(_this_file)

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.6.3"
+VERSION_NO = "0.6.4"

picasso/gui/average3.py

@@ -25,7 +25,6 @@
 from numpy.lib.recfunctions import stack_arrays
 
 from cmath import rect, phase
-from tqdm import tqdm
 
 import scipy.ndimage.filters
 import importlib, pkgutil
@@ -874,7 +873,7 @@ def translate(self, translateaxis):
             plt.plot(element)
         n_groups = self.group_index[0].shape[0]
         print("Translating..")
-        for i in tqdm(range(n_groups)):
+        for i in range(n_groups):
             self.status_bar.showMessage("Group {} / {}.".format(i, n_groups))
             self.translate_group(signalimg, i, translateaxis)
 
@@ -1221,7 +1220,7 @@ def rotatexy_convolution(self):
         CF_image_avg = image
 
         print("Convolving..")
-        for i in tqdm(range(n_groups)):
+        for i in range(n_groups):
             self.status_bar.showMessage("Group {} / {}.".format(i, n_groups))
             self.rotatexy_convolution_group(CF_image_avg, angles, i, rotaxis, proplane)
         self.updateLayout()
@@ -1360,7 +1359,7 @@ def rotate_groups(self):
         # image_half = n_pixel / 2
 
         print("Rotating..")
-        for i in tqdm(range(n_groups)):
+        for i in range(n_groups):
             self.status_bar.showMessage("Group {} / {}.".format(i, n_groups))
             self.align_group(CF_image_avg, angles, i, rotaxis, proplane)
         self.updateLayout()
@@ -1485,7 +1484,7 @@ def calculate_score(self):
         n_channels = len(image)
 
         print("Calculating score..")
-        for i in tqdm(range(n_groups)):
+        for i in range(n_groups):
             channel_score = []
             for j in range(n_channels):
                 if self.dataset_dialog.checks[j].isChecked():

picasso/gui/nanotron.py

@@ -13,7 +13,6 @@
 import sys
 import traceback
 import importlib, pkgutil
-from tqdm import tqdm
 import datetime
 from time import sleep
 
@@ -94,9 +93,7 @@ def run(self):
 
             export_path = _ospath.dirname(self.export_paths[id]) + "/"
 
-            for c, pick in enumerate(
-                tqdm(np.unique(locs.group), desc="Prepare class " + str(label))
-            ):
+            for c, pick in enumerate(np.unique(locs.group)):
 
                 pick_img = nanotron.roi_to_img(
                     locs=locs,

picasso/gui/render.py

@@ -10054,7 +10054,7 @@ def update_cursor(self):
                 diameter = int(self.width() * diameter / self.viewport_width())
                 # remote desktop crashes sometimes for high diameter
                 if diameter < 100:
-                    pixmap_size = ceil(diameter)
+                    pixmap_size = ceil(diameter) + 1
                     pixmap = QtGui.QPixmap(pixmap_size, pixmap_size)
                     pixmap.fill(QtCore.Qt.transparent)
                     painter = QtGui.QPainter(pixmap)

picasso/imageprocess.py

@@ -110,18 +110,25 @@ def rcc(segments, max_shift=None, callback=None):
     shifts_y = _np.zeros((n_segments, n_segments))
     n_pairs = int(n_segments * (n_segments - 1) / 2)
     flag = 0
-    with _tqdm(
-        total=n_pairs, desc="Correlating image pairs", unit="pairs"
-    ) as progress_bar:
-        if callback is not None:
-            callback(0)
+    if callback is None:
+        with _tqdm(
+            total=n_pairs, desc="Correlating image pairs", unit="pairs"
+        ) as progress_bar:
+            for i in range(n_segments - 1):
+                for j in range(i + 1, n_segments):
+                    progress_bar.update()
+                    shifts_y[i, j], shifts_x[i, j] = get_image_shift(
+                        segments[i], segments[j], 5, max_shift
+                    )
+                    flag += 1
+    else:
+        callback(0)
         for i in range(n_segments - 1):
             for j in range(i + 1, n_segments):
-                progress_bar.update()
                 shifts_y[i, j], shifts_x[i, j] = get_image_shift(
                     segments[i], segments[j], 5, max_shift
                 )
                 flag += 1
-                if callback is not None:
-                    callback(flag)
+                callback(flag)
+
     return _lib.minimize_shifts(shifts_x, shifts_y)

picasso/io.py

@@ -190,8 +190,8 @@ def load_movie(path, prompt_info=None, progress=None):
         return load_ims(path, prompt_info=prompt_info)
     elif ext == '.nd2':
         return load_nd2(path)
-    elif ext == ".tiff":
-        print("Extension .tiff not supported, please use .ome.tif instead.")
+    # elif ext == ".tiff":
+    #     print("Extension .tiff not supported, please use .ome.tif instead.")
 
 def load_info(path, qt_parent=None):
     path_base, path_extension = _ospath.splitext(path)

picasso/postprocess.py

@@ -1057,9 +1057,12 @@ def segment(locs, info, segmentation, kwargs={}, callback=None):
     n_seg = n_segments(info, segmentation)
     bounds = _np.linspace(0, n_frames - 1, n_seg + 1, dtype=_np.uint32)
     segments = _np.zeros((n_seg, Y, X))
-    if callback is not None:
+    if callback is None:
+        it = _trange(n_seg, desc="Generating segments", unit="segments")
+    else:
         callback(0)
-    for i in _trange(n_seg, desc="Generating segments", unit="segments"):
+        it = range(n_seg)
+    for i in it:
         segment_locs = locs[
             (locs.frame >= bounds[i]) & (locs.frame < bounds[i + 1])
         ]

release/one_click_windows_gui/create_installer_windows.bat

@@ -3,15 +3,15 @@ call DEL /F/Q/S dist > NUL
 call RMDIR /Q/S build
 call RMDIR /Q/S dist
 
-call cd %~dp0\..\..\..
+call cd %~dp0\..\..
 
 call conda create -n picasso_installer python=3.10 -y
 call conda activate picasso_installer
 
 call python setup.py sdist bdist_wheel
 
 call cd release/one_click_windows_gui
-call pip install "../../dist/picassosr-0.6.3-py3-none-any.whl"
+call pip install "../../dist/picassosr-0.6.4-py3-none-any.whl"
 
 call pip install pyinstaller==5.7
 call pyinstaller ../pyinstaller/picasso.spec -y --clean

release/one_click_windows_gui/picasso_innoinstaller.iss

@@ -1,10 +1,10 @@
 [Setup]
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
-AppVersion=0.6.3
+AppVersion=0.6.4
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.3"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.4"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="picassosr",
-    version="0.6.3",
+    version="0.6.4",
     author="Joerg Schnitzbauer, Maximilian T. Strauss, Rafal Kowalewski",
     author_email=("[email protected], [email protected], [email protected]"),
     url="https://github.com/jungmannlab/picasso",