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https://github.com/profLewis/geog0111_OLD

UCL Geography: 4th year course, Scientific Computing
https://github.com/profLewis/geog0111_OLD

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UCL Geography: 4th year course, Scientific Computing

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README 

        
# Welcome to geog0111: Scientific Computing 

UCL Geography: Level 7 course, Scientific Computing



![](images/ucl_logo.png)



[![Documentation Status](https://readthedocs.org/projects/geog0111/badge/?version=latest)](https://geog0111.readthedocs.io/en/latest/?badge=latest)



Online Notebooks via Binder:

----------------------------

 

Run the notebooks on Binder server directly by click on different

chaper, it may take some time to start but just wait a bit....

 

[Go to full list of

notebooks](https://mybinder.org/v2/gh/profLewis/geog0111/master)

 

Go to individual chapter:

 

[Chapter0\_help](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter0_help.ipynb)

 

[Chapter1\_Python\_introduction](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter1_Python_introduction.ipynb)

 

[Chapter1\_Python\_introduction\_answers](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter1_Python_introduction_answers.ipynb)

 

[Chapter2\_Numpy\_matplotlib](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter2_Numpy_matplotlib.ipynb)

 

[Chapter2\_Numpy\_matplotlib\_answers](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter2_Numpy_matplotlib_answers.ipynb)

 

[Chapter3\_0\_GDAL](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_0_GDAL.ipynb)

 

[Chapter3\_1\_GDAL](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_1_GDAL.ipynb)

 

[Chapter3\_1\_GDAL\_answers](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_1_GDAL_answers.ipynb)

 

[Chapter3\_2\_MODIS\_download](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_2_MODIS_download.ipynb)

 

[Chapter3\_2\_MODIS\_download\_answers](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_2_MODIS_download_answers.ipynb)

 

[Chapter3\_3\_GDAL\_masking](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_3_GDAL_masking.ipynb)

 

[Chapter3\_4\_GDAL\_stacking\_and\_interpolating](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_4_GDAL_stacking_and_interpolating.ipynb)

 

[Chapter3\_4a\_GDAL\_stacking\_and\_interpolating-convolution](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_4a_GDAL_stacking_and_interpolating-convolution.ipynb)

 

[Chapter3\_5\_Movies](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_5_Movies.ipynb)

 

[Chapter3\_6A\_GDAL\_Reconciling\_projections\_prerequisites](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_6A_GDAL_Reconciling_projections_prerequisites.ipynb)

 

[Chapter3\_6\_GDAL\_Reconciling\_projections](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter3_6_GDAL_Reconciling_projections.ipynb)

 

[Chapter4\_Practical\_Part1](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter4_Practical_Part1.ipynb)

 

[Chapter5\_Linear\_models](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter5_Linear_models.ipynb)

 

[Chapter5\_Modelling\_and\_optimisation](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter5_Modelling_and_optimisation.ipynb)

 

[Chapter6\_NonLinear\_Model\_Fitting](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter6_NonLinear_Model_Fitting.ipynb)

 

[Chapter6\_NonLinear\_Model\_Fitting\_Solutions](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter6_NonLinear_Model_Fitting_Solutions.ipynb)

 

[Chapter7\_FittingPhenologyModels](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter7_FittingPhenologyModels.ipynb)

 

[Chapter7\_FittingPhenologyModels\_Solutions](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter7_FittingPhenologyModels_Solutions.ipynb)

 

[Chapter8\_Practical\_Part2](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter8_Practical_Part2.ipynb)

 

[Chapter9\_Fire\_and\_Teleconnections](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter9_Fire_and_Teleconnections.ipynb)

 

[Chapter9\_Fire\_and\_Teleconnections\_Solution](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Chapter9_Fire_and_Teleconnections_Solution.ipynb)

 

[Connection](https://mybinder.org/v2/gh/profLewis/geog0111/master?filepath=Connection.ipynb)



## Course information



### Course Convenor



[Prof P. Lewis](http://www.geog.ucl.ac.uk/~plewis)



N.B. 2019-20 Course Convenors: [Dr Qingling Wu](http://www.geog.ucl.ac.uk/about-the-department/people/research-staff/research-staff/qingling-wu/) 



### Course and Contributing Staff



[Prof Philip Lewis](http://www.geog.ucl.ac.uk/~plewis)  



[Dr. Jose Gomez-Dans](http://www.geog.ucl.ac.uk/about-the-department/people/research-staff/research-staff/jose-gomez-dans/)



[Dr Qingling Wu](http://www.geog.ucl.ac.uk/about-the-department/people/research-staff/research-staff/qingling-wu/)



### Purpose of this course



This course, geog0111 Scientific Computing, is a term 1 MSc module worth 15 credits (25% of the term 1 credits) that aims to:



* impart an understanding of scientific computing

* give students a grounding in the basic principles of algorithm development and program construction

* to introduce principles of computer-based image analysis and model development



It is open to students from a number of MSc courses run by the Department of Geography UCL, but the material should be of wider value to others wishing to make use of scientific computing. 



The module will cover:



* Computing in Python

* Computing for image analysis

* Computing for environmental modelling

* Data visualisation for scientific applications



### Learning Outcomes



At the end of the module, students should:



* have an understanding of the Python programmibng language and experience of its use

* have an understanding of algorithm development and be able to use widely used scientific computing software to manipulate datasets and accomplish analytical tasks

* have an understanding of the technical issues specific to image-based analysis, model implementation and scientific visualisation



### Timetable



The course takes place over 10 weeks in term 1, in the Geography Department Unix Computing Lab (PB110) in the [Pearson Building](http://www.ucl.ac.uk/estates/roombooking/building-location/?id=003), UCL. 



Classes take place from the second week of term to the final week of term, other than Reading week. See UCL [term dates](http://www.ucl.ac.uk/staff/term-dates) for further information.



The timetable is available on the UCL Academic Calendar



### Assessment



Assessment is through two pieces of coursework, submitted in both paper form and electronically via Moodle. 



See the [Moodle page](https://moodle.ucl.ac.uk/course/view.php?id=2796) for more details.



### Useful links



[Course Moodle page](https://moodle.ucl.ac.uk/course/view.php?id=2796)  



### Python



[Python](http://www.python.org/) is a high level programming language that is freely available, relatively easy to learn and portable across different computing systems. In Python, you can rapidly develop solutions for the sorts of problems you might need to solve in your MSc courses and in the world beyond. Code written in Python is also easy to maintain, is (or should be) self-documented, and can easily be linked to code written in other languages.



Relevant features include: 



- it is automatically compiled and executed 

- code is portable provided you have the appropriate Python modules. 

- for compute intensive tasks, you can easily make calls to methods written in (faster) lower-level languages such as C or FORTRAN 

- there is an active user and development community, which means that new capabilities appear over time and there are many existing extensions and enhancements easily available to you.



For further background on Python, look over the material on [Advanced Scientific Programming in Python](https://python.g-node.org/wiki/schedule) or [python.org](http://www.python.org/) web sites.



We are assuming that you are new to computing in this course. We will not explicitly go through unix (operating system) notes, but you should make yourself familiar with the basic concepts. 



### Using the course notes



We will generally use the `jupyter` notebooks for running interactive Python programs.



You will probably want to run each session and store scripts in your `Data` (or `DATA`) directory.



If you are taking this course at UCL, the notes should already have been downloaded to your `DATA` directory.



If so, then:



```

cd /directory/to/geog0111

git reset --hard HEAD

git pull

```



will update the notes (for any changes I make over the sessions).



If you need to download the notes and want to run the session directly in the notebook, you will need to download the course material from [github](https://github.com/profLewis/geog0111) and run the notebook with e.g.:



```

cd /directory/to/

git clone https://github.com/profLewis/geog0111.git

```



to obtain the notes. 



### Using python



We suggest you use the [anaconda python distribution](http://www.anaconda.com). if you are *not* using the UCL resources (i.e. using your own comnputer), you should download and install an [anaconda distribution](https://www.anaconda.com/download). If you *are* using the UCL computers, then it should be there already.



You may also find it of value to have [git](http://git-scm.com/) installed.



Assuming you have a copy of the notes in the directory ('folder') `~/DATA/geog0111` then you can set up a specific 'environment' in which to run these notes:



```

cd /directory/to/geog0111

conda env create -f environment.yml

```



If you are updating the notes, and geog0111 already exists, use instead:



```

cd /directory/to/geog0111

conda env update -f environment.yml

```



This will create an environment called `geog0111` and make sure you have all of the required dependencies.



If you have created the environment, you can activate it with:



```

conda activate geog0111

python setup.py install

```



For further advice on checking, setting or deleting `conda` environments, see the [conda help pages](https://conda.io/docs/user-guide/tasks/manage-environments.html).



To go to the directory for the first session:  



`cd /directory/to/geog0111`  

`jupyter notebook Chapter1_Python_intro.ipynb`  



You quit an `jupyter` notebook session with `^C` (`Control C`).



To exectute ('run') blocks of Python code in the notebook, use `^` (`SHIFT` and `RETURN` keys together).



Alternatively, just run `ipython`:  

```

cd /directory/to/geog0111

ipython

```



and type your own commands in at the prompt, following the class or the material on the webpages.



### Course Notes



[Course notes](index.ipynb)  



### Help



[Help](Chapter0_help.ipynb)

[Connections to the lab](Connection.ipynb)