Leginon 1.2 available for download

Leginon 1.2.0 has been posted on the download page:

http://emg.nysbc.org/software/leginon/

There are three downloads available:

Leginon 1.2.0 (new)

pyScope 1.0.5 (you may already have this)

NumExtension 1.0.2 (you may already have this)

These are available as either tar.gz archives, which are platform independent, or Windows installer exe. We no longer provide packages for specific Linux distributions. Here is an example of installing Leginon from the tar.gz using Python distutils:

tar zxf Leginon-1.2.0.tar.gz
cd Leginon-1.2.0
python setup.py install

If you would rather create an RPM package and install from that:

tar zxf Leginon-1.2.0.tar.gz
cd Leginon-1.2.0
vi setup.cfg  (you may need to modify the dependency list depending on your distro)
python setup.py bdist_rpm
cd dist
rpm -Uvh Leginon-1.2.0-1.noarch.rpm

In addition to the three downloads from our website, there are several other requirements that you will get either from your OS installation source, or from its respective website. After installing leginon, you can automatically check your system to see if you already have these requirements. Start python and run the Leginon system check script (in this example, ">>>" is the python command prompt):

python
>>> import syscheck

If you see any lines like "*** Failed...", then you have something missing. Otherwise, everything should result in "OK". Here are the requirements and where you can get them (if your OS installation does not include it)

Python 2.3.4 or newer: http://www.python.org

wxPython 2.5.2.8 or newer: http://www.wxpython.org

MySQL Python client 1.2 or newer: http://sourceforge.net/projects/mysql-python

Python Imaging Library (PIL) 1.1.4 or newer: http://www.pythonware.com/products/pil/

numarray 1.1 or newer: http://www.stsci.edu/resources/software_hardware/numarray

Python XML module 0.8.3 or newer: http://pyxml.sourceforge.net

Note for Windows: you will need the pywin32 extensions: http://sourceforge.net/projects/pywin32/

Replies (12)

Leginon 1.2.0 Documentation is on line - Added by Anchi Cheng over 18 years ago

To Leginon users,

The manual updated for Leginon 1.2.0 is now available online.

On a separate note, I recommend highly that starting a user called "Administrator" for setting institution default for the new user, a new feature in v1.2, to reduce the confusion from new users at your institution.

Anchi

- Added by Jim Pulokas over 18 years ago

The windows installers for pyScope and NumExtension are only good for Python 2.3. I will add the Python 2.4 versions within the next couple of hours.

Jim

- Added by Anonymous over 18 years ago

I've started to have problems after upgrading to Leginon v.1.2.0. When I send a preset to the microscope (from the preset manager in the Calibration application), I get the error message "Preset change failed: unable to set instrument". This is despite the microscope apparently getting the parameters for the preset (magnification, defocus, etc). Also, acquiring the dose image does not work at all now - it fails because of the error from setting the preset,

William

- Added by Anonymous over 18 years ago

Another thing that may be a problem is that the buttons, etc in Focus/ Focus Sequence are greyed out so they can't be changed although the manual advises setting these to sensible defaults after upgrading,

William

- Added by Anonymous over 18 years ago

By the way, are there new versions of the applications - MSI, MSI-raster, Calibration and Manual - for version 1.2.0 of Leginon? Just MSI-H 1.2 is available for download on the Leginon page right now,

William

- Added by Anonymous over 18 years ago

"WVNicholson" wrote: I've started to have problems after upgrading to Leginon v.1.2.0. When I send a preset to the microscope (from the preset manager in the Calibration application), I get the error message "Preset change failed: unable to set instrument". This is despite the microscope apparently getting the parameters for the preset (magnification, defocus, etc). Also, acquiring the dose image does not work at all now - it fails because of the error from setting the preset,
William

I seem to have something working now with Leginon v.1.2.0 and the old pyScope 1.0.5. I'm not clear if the new pyScope was the problem or if it was because of old files from Leginon v1.1.3 (because I eventually ended up installing Leginon v.1.2.0 as a fresh install in Linux after erasing the previous v.1.1.3). Using Leginon v1.2.0 and the old pyScope 1.0.5 also avoids having to upgrade Python from v2.3 to v2.4 on Windows (as there isn't an installer for Python 2.3 available for PyScope 1.0.6),

William

- Added by Jim Pulokas over 18 years ago

I'll respond to each of your questions, although you may have already resolved some of them...

It sounds like the "Preset change failed" probably had something to do with pyScope, but I'm not sure what. Sometimes just reinstalling pyScope (or running its updatecom.py script) helps resolve these types of issues. Sorry about not having 1.0.6 for python 2.3. It is just more convenient for us to drop python 2.3 because we upgraded visual studio and now it won't let us compile any extensions for python 2.3. To build a 2.3 version of pyscope, we either have to downgrade our compiler or compile our own version of python. It is easier to just force people to upgrade to python 2.4, but if this causes too much trouble, we will reconsider. Python 2.4 has been around for over a year, so I figure it is time to start working with it exclusively.

In the Focuser node, do you mean that, for example, the "Enabled" checkbox and everything below it are greyed out? This is normal the first time you set it up after the upgrade, since you will not initially have anything in the database for this new layout. First you must add at least one item to the "Focus sequence" list box. Then you will be able to configure the options for that item. You may create as many items as you like. To reproduce the same behavior as Leginon 1.1, you would create three items: "pre manual", "auto", "post manual". (call them whatever you want)

The applications actually have not changed since 1.1, so you should be safe to use them. When we get them back online they will probably be called 1.2, but they are really the same.

Jim

- Added by Anonymous over 18 years ago

"pulokas" wrote: I'll respond to each of your questions, although you may have already resolved some of them...

It sounds like the "Preset change failed" probably had something to do with pyScope, but I'm not sure what. Sometimes just reinstalling pyScope (or running its updatecom.py script) helps resolve these types of issues. Sorry about not having 1.0.6 for python 2.3. It is just more convenient for us to drop python 2.3 because we upgraded visual studio and now it won't let us compile any extensions for python 2.3. To build a 2.3 version of pyscope, we either have to downgrade our compiler or compile our own version of python. It is easier to just force people to upgrade to python 2.4, but if this causes too much trouble, we will reconsider. Python 2.4 has been around for over a year, so I figure it is time to start working with it exclusively.

I tried upgrading to pyScope 1.0.6 again and also the microscope PC from Python 2.3 to 2.4. I still had the same problems despite doing this upgrade as a remove of pyScope and Leginon on both systems and then re-installing them (rather than as a proper upgrade). However, I was able to go back to pyScope 1.0.5 while keeping Python 2.4 on the Windows system so I suppose I will be ready for any future upgrades if you are not supporting Python 2.3 on Windows.
I don't understand how to use the updatecom.py script. Do I just run it without any arguments? Also, do I run it both on the main Leginon system and the microscope PC?

"pulokas" wrote:
In the Focuser node, do you mean that, for example, the "Enabled" checkbox and everything below it are greyed out? This is normal the first time you set it up after the upgrade, since you will not initially have anything in the database for this new layout. First you must add at least one item to the "Focus sequence" list box. Then you will be able to configure the options for that item. You may create as many items as you like. To reproduce the same behavior as Leginon 1.1, you would create three items: "pre manual", "auto", "post manual". (call them whatever you want)

Yes, the "enabled" checkbox and everything below are greyed out. I assumed this prevented me from adding any items to the "Focus sequence" list box as well. However, if I fill in the field for text input next to the add button then the add button becomes ungreyed,

William

- Added by Anonymous over 18 years ago

Okay, I tried yet another upgrade to pyScope 1.0.6 (on both the main Leginon system and the microscope PC). I ran updatecom.py after this upgrade (updatecom.py was just run on the microscope PC/ Windows system). Here is the output from running updatecom.py:

C:\Python24\Lib\site-packages\pyScope>updatecom.py

Generating .py files from type libraries...

Tecnai Scripting: Tecnai Scripting -> tecnaicom.py

Tecnai Low Dose Kit: Low Dose Server Library -> ldcom.py

Tecnai Exposure Adaptor: adaExp Library -> adacom.py

Gatan CCD Camera: TecnaiCCD 1.0 Type Library -> gatancom.py

Tietz CCD Camera: Error, cannot find typelib for "CAMC4 1.0 Type Library"

Done.

I still had the same problems with the presets that I described earlier,

William

"WVNicholson" wrote: > "pulokas" wrote: I'll respond to each of your questions, although you may have already resolved some of them...

It sounds like the "Preset change failed" probably had something to do with pyScope, but I'm not sure what. Sometimes just reinstalling pyScope (or running its updatecom.py script) helps resolve these types of issues. Sorry about not having 1.0.6 for python 2.3. It is just more convenient for us to drop python 2.3 because we upgraded visual studio and now it won't let us compile any extensions for python 2.3. To build a 2.3 version of pyscope, we either have to downgrade our compiler or compile our own version of python. It is easier to just force people to upgrade to python 2.4, but if this causes too much trouble, we will reconsider. Python 2.4 has been around for over a year, so I figure it is time to start working with it exclusively.

- Added by Anonymous over 18 years ago

It's also been noticed that when the pyScope 1.0.6 upgrade is carried out then the microscope icon for the Instrument node does not appear when the Leginon client is started up on the microscope PC,

William

"WVNicholson" wrote: Okay, I tried yet another upgrade to pyScope 1.0.6 (on both the main Leginon system and the microscope PC). I ran updatecom.py after this upgrade (updatecom.py was just run on the microscope PC/ Windows system). Here is the output from running updatecom.py:

C:\Python24\Lib\site-packages\pyScope>updatecom.py
Generating .py files from type libraries...
Tecnai Scripting: Tecnai Scripting -> tecnaicom.py
Tecnai Low Dose Kit: Low Dose Server Library -> ldcom.py
Tecnai Exposure Adaptor: adaExp Library -> adacom.py
Gatan CCD Camera: TecnaiCCD 1.0 Type Library -> gatancom.py
Tietz CCD Camera: Error, cannot find typelib for "CAMC4 1.0 Type Library"
Done.

I still had the same problems with the presets that I described earlier,
William

"WVNicholson" wrote: > "pulokas" wrote: I'll respond to each of your questions, although you may have already resolved some of them...

It sounds like the "Preset change failed" probably had something to do with pyScope, but I'm not sure what. Sometimes just reinstalling pyScope (or running its updatecom.py script) helps resolve these types of issues. Sorry about not having 1.0.6 for python 2.3. It is just more convenient for us to drop python 2.3 because we upgraded visual studio and now it won't let us compile any extensions for python 2.3. To build a 2.3 version of pyscope, we either have to downgrade our compiler or compile our own version of python. It is easier to just force people to upgrade to python 2.4, but if this causes too much trouble, we will reconsider. Python 2.4 has been around for over a year, so I figure it is time to start working with it exclusively.

- Added by Jim Pulokas over 18 years ago

hopefully I will have some time to test this today on our Gatan system. Most of our testing is done on the Tietz system, and that has been working fine with 1.0.6 for a few weeks.

- Added by Jim Pulokas over 18 years ago

I have finally tested pyScope 1.0.6 on our Gatan system and unfortunately I could not reproduce any problems. Please see the new topic "pyScope 1.0.6 problems" where I will try to figure out what the problem is.

(1-12/12)

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