fixing bug with save_server (MouseLand#467) and adding docs for cuda …

…toolkit 10

README.md

@@ -117,7 +117,6 @@ You can also try to install cellpose, omnipose and the GUI dependencies from you
 python -m pip install cellpose[all]
 ~~~~
 
-
 If you have **issues** with installation, see the [docs](https://cellpose.readthedocs.io/en/latest/installation.html) for more details. You can also use the cellpose environment file included in the repository and create a cellpose environment with `conda env create -f environment.yml` which may solve certain dependency issues.
 
 If these suggestions fail, open an issue.
@@ -131,10 +130,10 @@ Before installing the GPU version, remove the CPU version:
 pip uninstall torch
 ~~~
 
-Follow the instructions [here](https://pytorch.org/get-started/locally/) to determine what version to install. The Anaconda install is strongly recommended, and then choose the CUDA version that is supported by your GPU (newer GPUs may need newer CUDA versions > 10.2). For instance this command will install the 10.2 version on Linux and Windows (note the `torchvision` and `torchaudio` commands are removed because cellpose doesn't require them):
+Follow the instructions [here](https://pytorch.org/get-started/locally/) to determine what version to install. The Anaconda install is strongly recommended, and then choose the CUDA version that is supported by your GPU (newer GPUs may need newer CUDA versions > 10.2). For instance this command will install the 11.3 version on Linux and Windows (note the `torchvision` and `torchaudio` commands are removed because cellpose doesn't require them):
 
 ~~~
-conda install pytorch cudatoolkit=10.2 -c pytorch
+conda install pytorch cudatoolkit=11.3 -c pytorch
 ~~~~
 
 ### Installation of github version

cellpose/io.py

@@ -9,6 +9,7 @@
 
 try:
  from PyQt5 import QtGui, QtCore, Qt, QtWidgets
+ from PyQt5.QtWidgets import QMessageBox
  GUI = True
 except:
  GUI = False
@@ -480,13 +481,13 @@ def save_server(parent=None, filename=None):
  if no GUI, send this file to server
  """
  if parent is not None:
- q = QtGui.QMessageBox.question(
+ q = QMessageBox.question(
  parent,
  "Send to server",
  "Are you sure? Only send complete and fully manually segmented data.\n (do not send partially automated segmentations)",
- QtGui.QMessageBox.Yes | QtGui.QMessageBox.No
+ QMessageBox.Yes | QMessageBox.No
  )
- if q != QtGui.QMessageBox.Yes:
+ if q != QMessageBox.Yes:
  return
  else:
  filename = parent.filename

cellpose/models.py

@@ -135,7 +135,7 @@ def eval(self, x, batch_size=8, channels=None, channel_axis=None, z_axis=None,
  invert image pixel intensity before running network (if True, image is also normalized)
 
  normalize: bool (optional, default True)
-  normalize data so 0.0=1st percentile and 1.0=99th percentile of image intensities in each channel
+ normalize data so 0.0=1st percentile and 1.0=99th percentile of image intensities in each channel
 
  diameter: float (optional, default 30.)
  if set to None, then diameter is automatically estimated if size model is loaded

docs/installation.rst

@@ -33,6 +33,15 @@ this code at the beginning of your notebook before you import cellpose:
 Common issues
 ~~~~~~~~~~~~~~~~~~~~~~~
 
+If you are having issues with CUDA on Windows, or want to use 
+Cuda Toolkit 10, please follow these `instructions <https://github.com/MouseLand/cellpose/issues/481#issuecomment-1080137885>`_:
+
+::
+ 
+ conda create -n cellpose pytorch=1.8.2 cudatoolkit=10.2 -c pytorch-lts
+ conda activate cellpose
+ pip install cellpose
+
 If you receive the error: ``No module named PyQt5.sip``, then try
 uninstalling and reinstalling pyqt5