Hi Matt,
There is some information about how to install Python packages with Chimera in the programming FAQ
https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b
but I believe Eric here said the suggested approach to doing pip install no longer works. A more hacky approach is to simply copy site-packages/Mido (or whatever the module is called) from your system installed version into the Chimera Python site-packages (in chimera/lib/python2.7/site-packages or Chimera.app/Contents/Resources/lib/python2.7/site-packages on Mac).
Tom
On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T matthewd@bcm.edu wrote:
I have looked around at python midi packages. I think I can get around modifying the tk/qt event loops by polling the midi port.
I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment.
To install the Mido library into chimera, what do you recommend?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Sent: Monday, November 21, 2016 12:53:04 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu mailto:chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] ChimeraX
***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. Hi Matt,
The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library
https://github.com/waddlesplash/QMidi https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplash_QMidi&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=9_fN2otNCHI9eFtt4LSxl9b9nKrTFPjcRM6Gzi-8bsg&e=
which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX.
We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing.
Tom
On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote:
Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry.
For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform.
For complex devices such as DS1, midi appears to be the best method for dial boxes. There is also economical advantages and an ongoing evolution of such devices. https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEWM... https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2DInstruments-2DPortable-2DDigital-2DMixer_dp_B00M4OEWMW_ref-3Dsr-5F1-5F1-3Fie-3DUTF8-26qid-3D1479490715-26sr-3D8-2D1-26keywords-3Dlivid-2Bds1&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=kwBeFxV6UE7XEm6Mrx9c5rzqHCfSaEjuTGoMCjd7VCI&e=
It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons).
We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX.
Any further ideas?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=D3cEWzb75IuNwX7g2k7vByJLT2jh77niD82hK0wgB88&e=
hi matthew,
for development you can use the pip of chimerax to install external tools, but pip is not directly accessible: ChimeraX -m pip install ... or ${CHIMERAX}/bin/python3.5 ${CHIMERAX}/lib/python3.5/site-packages/pip install ... CHIMERAX points to my installationpath on the harddisk and the package finally goes into the chimerax python tree. the second method does not refresh the chimerax cache.
but maybe its better to put the dependency into the deployment of your tool in setup.py (e.g. i need pyparsing by pip): install_requires=['pyparsing', 'ChimeraX-Core>=0.1'],
cheers, wolfgang
On 01/14/2017 03:38 AM, Tom Goddard wrote:
On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T <matthewd@bcm.edu mailto:matthewd@bcm.edu> wrote:
I have looked around at python midi packages. I think I can get around modifying the tk/qt event loops by polling the midi port.
I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment.
To install the Mido library into chimera, what do you recommend?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
*From:*Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> *Sent:*Monday, November 21, 2016 12:53:04 PM *To:*Dougherty, Matthew T *Cc:*chimera-dev@cgl.ucsf.edu mailto:chimera-dev@cgl.ucsf.edu *Subject:*Re: [chimera-dev] ChimeraX ****CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.*
Hi Matt,
The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library
https://github.com/waddlesplash/QMidi https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplash_QMidi&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=9_fN2otNCHI9eFtt4LSxl9b9nKrTFPjcRM6Gzi-8bsg&e=
which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX.
We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing.
Tom
On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote:
Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry.
For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform.
For complex devices such as DS1, midi appears to be the best method for dial boxes.There is also economical advantages and an ongoing evolution of such devices. https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEWM... https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2DInstruments-2DPortable-2DDigital-2DMixer_dp_B00M4OEWMW_ref-3Dsr-5F1-5F1-3Fie-3DUTF8-26qid-3D1479490715-26sr-3D8-2D1-26keywords-3Dlivid-2Bds1&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=kwBeFxV6UE7XEm6Mrx9c5rzqHCfSaEjuTGoMCjd7VCI&e=
It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons).
We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX.
Any further ideas?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=D3cEWzb75IuNwX7g2k7vByJLT2jh77niD82hK0wgB88&e=
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Tom,
I am planning to use the h5py library.
Referring to the email 1/13/17, I was wondering what would be the best route.
Looking at the h5py website: http://docs.h5py.org/en/latest/build.html
not sure if I should go with a preconfigured or the source install. pre-configured is what they recommend, I not making any changes for Mac, but not clear if I should do this for chimera.
Looking at the download area, https://pypi.python.org/pypi/h5py/2.7.0
the python library is in whl format
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________ From: Tom Goddard goddard@sonic.net Sent: Friday, January 13, 2017 8:38:56 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] ChimeraX
Hi Matt,
There is some information about how to install Python packages with Chimera in the programming FAQ
https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3bhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_ProgrammersGuide_faq.html-23q3b&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=s5qAVmF9zmMDL9NYLkHBPGWH46D1Q7DG_mOEXbHpQ4w&s=h0s58KLyIgJOslR1p0LWNV4MNf5XxvgSXy72X8XFL10&e=
but I believe Eric here said the suggested approach to doing pip install no longer works. A more hacky approach is to simply copy site-packages/Mido (or whatever the module is called) from your system installed version into the Chimera Python site-packages (in chimera/lib/python2.7/site-packages or Chimera.app/Contents/Resources/lib/python2.7/site-packages on Mac).
Tom
On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T <matthewd@bcm.edumailto:matthewd@bcm.edu> wrote:
I have looked around at python midi packages. I think I can get around modifying the tk/qt event loops by polling the midi port.
I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment.
To install the Mido library into chimera, what do you recommend?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Monday, November 21, 2016 12:53:04 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edumailto:chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] ChimeraX
***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. ________________________________ Hi Matt,
The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library
https://github.com/waddlesplash/QMidihttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplash_QMidi&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=9_fN2otNCHI9eFtt4LSxl9b9nKrTFPjcRM6Gzi-8bsg&e=
which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX.
We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing.
Tom
On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote:
Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry.
For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform.
For complex devices such as DS1, midi appears to be the best method for dial boxes. There is also economical advantages and an ongoing evolution of such devices. https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEWM...https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2DInstruments-2DPortable-2DDigital-2DMixer_dp_B00M4OEWMW_ref-3Dsr-5F1-5F1-3Fie-3DUTF8-26qid-3D1479490715-26sr-3D8-2D1-26keywords-3Dlivid-2Bds1&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=kwBeFxV6UE7XEm6Mrx9c5rzqHCfSaEjuTGoMCjd7VCI&e=
It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons).
We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX.
Any further ideas?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edumailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-devhttps://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=D3cEWzb75IuNwX7g2k7vByJLT2jh77niD82hK0wgB88&e=
Go with preconfigured if that is what they recommend. Use pip install as described in the January 13 message and see if it works. I don’t know if the wheel includes the HDF5 libraries. Chimera includes HDF5 libraries (version 1.8.9) in chimera/lib. Maybe h5py will use these or include its own.
Tom
On Apr 10, 2017, at 5:32 PM, Dougherty, Matthew T matthewd@bcm.edu wrote:
Hi Tom,
I am planning to use the h5py library.
Referring to the email 1/13/17, I was wondering what would be the best route.
Looking at the h5py website: http://docs.h5py.org/en/latest/build.html http://docs.h5py.org/en/latest/build.html
not sure if I should go with a preconfigured or the source install. pre-configured is what they recommend, I not making any changes for Mac, but not clear if I should do this for chimera.
Looking at the download area, https://pypi.python.org/pypi/h5py/2.7.0 https://pypi.python.org/pypi/h5py/2.7.0 the python library is in whl format
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= From: Tom Goddard goddard@sonic.net Sent: Friday, January 13, 2017 8:38:56 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] ChimeraX
Hi Matt,
There is some information about how to install Python packages with Chimera in the programming FAQ
https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_ProgrammersGuide_faq.html-23q3b&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=s5qAVmF9zmMDL9NYLkHBPGWH46D1Q7DG_mOEXbHpQ4w&s=h0s58KLyIgJOslR1p0LWNV4MNf5XxvgSXy72X8XFL10&e=
but I believe Eric here said the suggested approach to doing pip install no longer works. A more hacky approach is to simply copy site-packages/Mido (or whatever the module is called) from your system installed version into the Chimera Python site-packages (in chimera/lib/python2.7/site-packages or Chimera.app/Contents/Resources/lib/python2.7/site-packages on Mac).
Tom
On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T <matthewd@bcm.edu mailto:matthewd@bcm.edu> wrote:
I have looked around at python midi packages. I think I can get around modifying the tk/qt event loops by polling the midi port.
I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment.
To install the Mido library into chimera, what do you recommend?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Sent: Monday, November 21, 2016 12:53:04 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu mailto:chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] ChimeraX
***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. Hi Matt,
The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library
https://github.com/waddlesplash/QMidi https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplash_QMidi&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=9_fN2otNCHI9eFtt4LSxl9b9nKrTFPjcRM6Gzi-8bsg&e=
which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX.
We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing.
Tom
On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote:
Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry.
For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform.
For complex devices such as DS1, midi appears to be the best method for dial boxes. There is also economical advantages and an ongoing evolution of such devices. https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEWM... https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2DInstruments-2DPortable-2DDigital-2DMixer_dp_B00M4OEWMW_ref-3Dsr-5F1-5F1-3Fie-3DUTF8-26qid-3D1479490715-26sr-3D8-2D1-26keywords-3Dlivid-2Bds1&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=kwBeFxV6UE7XEm6Mrx9c5rzqHCfSaEjuTGoMCjd7VCI&e=
It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons).
We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX.
Any further ideas?
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=D3cEWzb75IuNwX7g2k7vByJLT2jh77niD82hK0wgB88&e=
participants (3)
-
Dougherty, Matthew T -
Tom Goddard -
Wolfgang Lugmayr