From 1d61d96571f11ca8bf622c4ca2577ad192202426 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Sun, 18 Feb 2018 13:39:54 +0000
Subject: [PATCH] minor updates based on talk practice
---
talks/packages/packages.ipynb | 69 +++++------------------------------
talks/packages/packages.md | 58 +++++------------------------
2 files changed, 18 insertions(+), 109 deletions(-)
diff --git a/talks/packages/packages.ipynb b/talks/packages/packages.ipynb
index 7d179c4..934f6f3 100644
--- a/talks/packages/packages.ipynb
+++ b/talks/packages/packages.ipynb
@@ -78,6 +78,9 @@
"source": [
"Tutorials for all sub-packages can be found [here](https://docs.scipy.org/doc/scipy-1.0.0/reference/).\n",
"\n",
+ "Alternative for `scipy.ndimage`:\n",
+ "- [Scikit-image](http://scikit-image.org/docs/stable/auto_examples/) for image manipulation/segmentation/feature detection\n",
+ "\n",
"## [Matplotlib](https://matplotlib.org/): Main plotting library"
]
},
@@ -865,50 +868,15 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Alternative: [pystan](https://pystan.readthedocs.io/en/latest/): wrapper around the [Stan](http://mc-stan.org/users/) probabilistic programming language.\n",
+ "Alternatives:\n",
+ "- [pystan](https://pystan.readthedocs.io/en/latest/): wrapper around the [Stan](http://mc-stan.org/users/) probabilistic programming language.\n",
+ "- [emcee](http://dfm.io/emcee/current/): if you just want MCMC\n",
"\n",
"\n",
"## [Pycuda](https://documen.tician.de/pycuda/): Programming the GPU\n",
"Wrapper around [Cuda](https://developer.nvidia.com/cuda-zone).\n",
- "The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/)."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "import pycuda.autoinit\n",
- "import pycuda.driver as drv\n",
- "\n",
- "from pycuda.compiler import SourceModule\n",
- "mod = SourceModule(\"\"\"\n",
- "__global__ void multiply_them(double *dest, double *a, double *b)\n",
- "{\n",
- " const int i = threadIdx.x;\n",
- " dest[i] = a[i] * b[i];\n",
- "}\n",
- "\"\"\")\n",
- "\n",
- "multiply_them = mod.get_function(\"multiply_them\")\n",
- "\n",
- "a = np.random.randn(400)\n",
- "b = np.random.randn(400)\n",
- "\n",
- "dest = np.zeros_like(a)\n",
- "multiply_them(\n",
- " drv.Out(dest), drv.In(a), drv.In(b),\n",
- " block=(400,1,1), grid=(1,1))\n",
- "\n",
- "print(dest-a*b)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Also see [pyopenGL](http://pyopengl.sourceforge.net/): graphics programming in python (used in FSLeyes)\n",
+ "- The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/).\n",
+ "- Also see [pyopenGL](http://pyopengl.sourceforge.net/): graphics programming in python (used in FSLeyes)\n",
"## Testing\n",
"- [unittest](https://docs.python.org/3.6/library/unittest.html): python built-in testing"
]
@@ -1079,6 +1047,7 @@
"- [trimesh](https://github.com/mikedh/trimesh): Triangular mesh algorithms\n",
"- [Pillow](https://pillow.readthedocs.io/en/latest/): Read/write/manipulate a wide variety of images (png, jpg, tiff, etc.)\n",
"- [psychopy](http://www.psychopy.org/): equivalent of psychtoolbox (workshop coming up in April in Nottingham)\n",
+ "- [Sphinx](http://www.sphinx-doc.org/en/master/): documentation generator\n",
"- [Buit-in libraries](https://docs.python.org/3/py-modindex.html)\n",
" - [collections](https://docs.python.org/3.6/library/collections.html): deque, OrderedDict, namedtuple, and more\n",
" - [datetime](https://docs.python.org/3/library/datetime.html): Basic date and time types\n",
@@ -1093,29 +1062,9 @@
" - [shutil](https://docs.python.org/3/library/shutil.html): copy/move files\n",
" - [subprocess](https://docs.python.org/3/library/subprocess.html): call shell commands\n",
" - [time](https://docs.python.org/3/library/time.html)/[timeit](https://docs.python.org/3/library/timeit.html): Timing your code\n",
- " - [turtle](https://docs.python.org/3/library/turtle.html#module-turtle): teach python to your kids!\n",
" - [warnings](https://docs.python.org/3/library/warnings.html#module-warnings): tell people they are not using your code properly"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "from turtle import *\n",
- "color('red', 'yellow')\n",
- "begin_fill()\n",
- "speed(10)\n",
- "while True:\n",
- " forward(200)\n",
- " left(170)\n",
- " if abs(pos()) < 1:\n",
- " break\n",
- "end_fill()\n",
- "done()"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
diff --git a/talks/packages/packages.md b/talks/packages/packages.md
index e72e5bd..4a2471b 100644
--- a/talks/packages/packages.md
+++ b/talks/packages/packages.md
@@ -39,6 +39,9 @@ optimize.minimize(costfunc, x0=[0], method='l-bfgs-b')
Tutorials for all sub-packages can be found [here](https://docs.scipy.org/doc/scipy-1.0.0/reference/).
+Alternative for `scipy.ndimage`:
+- [Scikit-image](http://scikit-image.org/docs/stable/auto_examples/) for image manipulation/segmentation/feature detection
+
## [Matplotlib](https://matplotlib.org/): Main plotting library
```
import matplotlib as mpl
@@ -552,39 +555,15 @@ _ = pm.traceplot(trace)
pm.summary(trace)
```
-Alternative: [pystan](https://pystan.readthedocs.io/en/latest/): wrapper around the [Stan](http://mc-stan.org/users/) probabilistic programming language.
+Alternatives:
+- [pystan](https://pystan.readthedocs.io/en/latest/): wrapper around the [Stan](http://mc-stan.org/users/) probabilistic programming language.
+- [emcee](http://dfm.io/emcee/current/): if you just want MCMC
## [Pycuda](https://documen.tician.de/pycuda/): Programming the GPU
Wrapper around [Cuda](https://developer.nvidia.com/cuda-zone).
-The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/).
-```
-import pycuda.autoinit
-import pycuda.driver as drv
-
-from pycuda.compiler import SourceModule
-mod = SourceModule("""
-__global__ void multiply_them(double *dest, double *a, double *b)
-{
- const int i = threadIdx.x;
- dest[i] = a[i] * b[i];
-}
-""")
-
-multiply_them = mod.get_function("multiply_them")
-
-a = np.random.randn(400)
-b = np.random.randn(400)
-
-dest = np.zeros_like(a)
-multiply_them(
- drv.Out(dest), drv.In(a), drv.In(b),
- block=(400,1,1), grid=(1,1))
-
-print(dest-a*b)
-```
-
-Also see [pyopenGL](http://pyopengl.sourceforge.net/): graphics programming in python (used in FSLeyes)
+- The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/).
+- Also see [pyopenGL](http://pyopengl.sourceforge.net/): graphics programming in python (used in FSLeyes)
## Testing
- [unittest](https://docs.python.org/3.6/library/unittest.html): python built-in testing
```
@@ -710,37 +689,18 @@ There are also many, many libraries to interact with databases, but you will hav
- [trimesh](https://github.com/mikedh/trimesh): Triangular mesh algorithms
- [Pillow](https://pillow.readthedocs.io/en/latest/): Read/write/manipulate a wide variety of images (png, jpg, tiff, etc.)
- [psychopy](http://www.psychopy.org/): equivalent of psychtoolbox (workshop coming up in April in Nottingham)
+- [Sphinx](http://www.sphinx-doc.org/en/master/): documentation generator
- [Buit-in libraries](https://docs.python.org/3/py-modindex.html)
- - [collections](https://docs.python.org/3.6/library/collections.html): deque, OrderedDict, namedtuple, and more
- - [datetime](https://docs.python.org/3/library/datetime.html): Basic date and time types
- [functools](https://docs.python.org/3/library/functools.html): caching, decorators, and support for functional programming
- [json](https://docs.python.org/3/library/json.html)/[ipaddress](https://docs.python.org/3/library/ipaddress.html)/[xml](https://docs.python.org/3/library/xml.html#module-xml): parsing/writing
- - [itertools](https://docs.python.org/3/library/itertools.html): more tools to loop over sequences
- [logging](https://docs.python.org/3/library/logging.htm): log your output to stdout or a file (more flexible than print statements)
- [multiprocessing](https://docs.python.org/3/library/multiprocessing.html)
- [os](https://docs.python.org/3/library/os.html#module-os)/[sys](https://docs.python.org/3/library/sys.html): Miscellaneous operating system interfaces
- [os.path](https://docs.python.org/3/library/os.path.html)/[pathlib](https://docs.python.org/3/library/pathlib.html): utilities to deal with filesystem paths (latter provides an object-oriented interface)
- [pickle](https://docs.python.org/3/library/pickle.html): Store/load any python object
- - [shutil](https://docs.python.org/3/library/shutil.html): copy/move files
- [subprocess](https://docs.python.org/3/library/subprocess.html): call shell commands
- - [time](https://docs.python.org/3/library/time.html)/[timeit](https://docs.python.org/3/library/timeit.html): Timing your code
- - [turtle](https://docs.python.org/3/library/turtle.html#module-turtle): teach python to your kids!
- [warnings](https://docs.python.org/3/library/warnings.html#module-warnings): tell people they are not using your code properly
-```
-from turtle import *
-color('red', 'yellow')
-begin_fill()
-speed(10)
-while True:
- forward(200)
- left(170)
- if abs(pos()) < 1:
- break
-end_fill()
-done()
-```
-
```
import this
```
--
GitLab