Focus Documentation

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1_0:external-tools [2018/01/24 14:56]
rdrighetto [Python] 		1_0:external-tools [2022/02/02 17:26] (current)
admin [Python and PILLOW]
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 The softwares in this category are compulsory and MUST be installed independent of anything. The softwares in this category are compulsory and MUST be installed independent of anything.
  
-==== CSH ==== +==== (t)CSH ==== 
-CSH is the language of programming for scripts. One would not be able to run anything without CSH. It is already present on most of the systems, if not please install TCSH >6.0.+CSH is a Unix shell and a scripting language widely used in the electron microscopy field for historical reasons. One would not be able to run anything from FOCUS without CSH. FOCUS requires its successor, TCSH, which is better and safer. In modern Linux distributions, **csh** is just a symbolic link to **tcsh**. Please make sure this is the case in your system. If not please install **tcsh** >6.0 and make sure that **csh** links to it.
  
-==== Python ====+==== gawk ==== 
 +gawk is a more powerful version of the command-line utility awk. Install gawk on OSX with "brew install gawk". On Linux, try "sudo apt-get install gawk".  
 + 
 +==== Python  and PILLOW ====
 Many utilities and specific-purpose tools used by FOCUS are written in the [[http://ww.python.org|Python]] scripting language (version 2.7.x). We recommend using a scientific Python installation like [[http://www.anaconda.com|Anaconda]] or [[http://www.enthought.com/product/canopy/|Canopy]]. You can also use the [[http://blake.bcm.edu/emanwiki/EMAN2|EMAN2.2]] Python environment based on Anaconda (see below). Many utilities and specific-purpose tools used by FOCUS are written in the [[http://ww.python.org|Python]] scripting language (version 2.7.x). We recommend using a scientific Python installation like [[http://www.anaconda.com|Anaconda]] or [[http://www.enthought.com/product/canopy/|Canopy]]. You can also use the [[http://blake.bcm.edu/emanwiki/EMAN2|EMAN2.2]] Python environment based on Anaconda (see below).
  
-=== MRCZ ===+You also need **pip** and the module **pil** (or **pillow**).  
 + 
 +On OSX, try  
 + 
 +// 
 +<nowiki> 
 +     xcode-select --install 
 +</nowiki> 
 +// 
 + 
 +// 
 +<nowiki> 
 +     brew install python2.7 
 +</nowiki> 
 +// 
 + 
 +// 
 +<nowiki> 
 +     pip3 install pillow 
 +</nowiki> 
 +// 
 + 
 +or alternatively: 
 + 
 +// 
 +<nowiki> 
 +     pip install pillow 
 +</nowiki> 
 +// 
 + 
 +On Linux, try: 
 +  * apt-get install python2.7 (or //yum install python2.7//) 
 +  * apt-get install python3 
 +  * pip3 install pillow 
 +  * pip3 install matplotlib 
 + 
 +and make sure in the Preferences panel of FOCUS, that FOCUS is using this python2.7 binary, which may reside in /usr/local/bin/python2.7 
 + 
 +Or to install those in python2.7:  
 +  * /usr/bin/python -mpip install -U pillow 
 +  * /usr/bin/python -mpip install -U matplotlib 
  
-Many of the Python scripts called within FOCUS rely on the [[http://github.com/em-MRCZ/python-mrcz|Python-MRCZ]] package. You can install ''mrcz'' in your Python environment with the following ''pip'' command:+==== MRCZ ==== 
 +Many of the Python scripts called within FOCUS rely on the [[http://github.com/em-MRCZ/python-mrcz|Python-MRCZ]] module. You can install ''mrcz'' in your Python environment with the following ''pip'' command:
  
 ''pip install mrcz'' ''pip install mrcz''
 +
 +Please ensure you have a version >= 0.5.1 of ''mrcz''.
 +
 +==== NumExpr ====
 +For accelerating some heavy calculations in Python scripts, FOCUS uses the [[https://numexpr.readthedocs.io|NumExpr]] evaluator. You can install ''numexpr'' in your Python environment with the following ''pip'' command:
 +
 +''pip install numexpr''
  
 ==== EMAN2 ==== ==== EMAN2 ====
 [[http://blake.bcm.edu/emanwiki/EMAN2|EMAN2]]  is a great package with lots of tools available. We might not use the tools present in EMAN2 directly, but we definitely use python distribution attached with the source. EMAN2 is easy to install and is available for MacOS and Linux on their website: http://blake.bcm.edu/emanwiki/EMAN2 [[http://blake.bcm.edu/emanwiki/EMAN2|EMAN2]]  is a great package with lots of tools available. We might not use the tools present in EMAN2 directly, but we definitely use python distribution attached with the source. EMAN2 is easy to install and is available for MacOS and Linux on their website: http://blake.bcm.edu/emanwiki/EMAN2
  
 +If you want to use the EMAN2 python (that is python 2.7), then you can link that python in the FOCUS Preferences dialogue, on **MacOS** for example as  /Applications/EMAN2/bin/python2.7 (or, where-ever you installed EMAN2). 
 +
 +If you compile FOCUS from source (which is recommended), sure that the ''build_all'' script does not accidentally use the EMAN2 version of qmake. You can test this by typing in a terminal ''which qmake'', or ''qmake ''''-''''-version'', to see, which qmake shows up first in your path. If the EMAN2 qmake is taken first, you might want to rename that to a different qmake name, such as "qmake-4.8.7".
 ==== IMOD ==== ==== IMOD ====
 We directly use many command line utilities present in IMOD. It can be downloaded from the website: http://bio3d.colorado.edu/imod/ We directly use many command line utilities present in IMOD. It can be downloaded from the website: http://bio3d.colorado.edu/imod/
  
 ==== CCP4 (Only for 2D crystallography projects) ==== ==== CCP4 (Only for 2D crystallography projects) ====
-Focus uses CPP4 in order to generate merged maps of the protein in 2D crystallography projects. The software can be downloaded from http://www.ccp4.ac.uk/download.php. Please follow their installation guide.+Focus uses CCP4 in order to generate merged maps of the protein in 2D crystallography projects. The software can be downloaded from http://www.ccp4.ac.uk/download.php. Please follow their installation guide.
  
 ===== Software for drift correction ===== ===== Software for drift correction =====
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 For a hastle-free data transfer for remote monitoring, you would need to install following software: For a hastle-free data transfer for remote monitoring, you would need to install following software:
   * cadaver: Available with all the package managers   * cadaver: Available with all the package managers
-