Differences

This shows you the differences between two versions of the page.

--- 1_0:external-tools [2018/05/19 22:53]
admin [EMAN2]
+++ 1_0:external-tools [2022/02/02 17:26] (current)
admin [Python and PILLOW]
@@ Line 5: / Line 5: @@
 The softwares in this category are compulsory and MUST be installed independent of anything.
-==== CSH ====
+==== (t)CSH ====
-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. It is already present on most systems, if not please install its improved successor, 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).
@@ Line 14: / Line 17: @@
 On OSX, try
-  * xcode-select --install
-  * brew install python@2
+//
-  * pip2 install pillow
+<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//)
-  * pip install pillow
+  * 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
-==== 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".
+Or to install those in python2.7:
+  * /usr/bin/python -mpip install -U pillow
+  * /usr/bin/python -mpip install -U matplotlib
 ==== MRCZ ====
-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:
+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''
+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 ====