diff --git a/getting_started/basics.ipynb b/getting_started/01_basics.ipynb
similarity index 56%
rename from getting_started/basics.ipynb
rename to getting_started/01_basics.ipynb
index 4cd6d7951303564e791df3d80c95220afd2ce159..a3210a7e20a0249eb372f786bdbd83688074a0d2 100644
--- a/getting_started/basics.ipynb
+++ b/getting_started/01_basics.ipynb
@@ -30,17 +30,9 @@
},
{
"cell_type": "code",
- "execution_count": 63,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "4\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = 4\n",
"b = 3.6\n",
@@ -59,19 +51,9 @@
},
{
"cell_type": "code",
- "execution_count": 64,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30]\n",
- "{'b': 20, 'a': 10}\n",
- "4 3.6 abc\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(d)\n",
"print(e)\n",
@@ -100,17 +82,9 @@
},
{
"cell_type": "code",
- "execution_count": 65,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "test string :: another test string\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"s1 = \"test string\"\n",
"s2 = 'another test string'\n",
@@ -126,20 +100,9 @@
},
{
"cell_type": "code",
- "execution_count": 66,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "This is\n",
- "a string over\n",
- "multiple lines\n",
- "\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"s3 = '''This is\n",
"a string over\n",
@@ -159,18 +122,9 @@
},
{
"cell_type": "code",
- "execution_count": 67,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "The numerical value is 1 and a name is PyTreat\n",
- "A name is PyTreat and a number is 1\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"x = 1\n",
"y = 'PyTreat'\n",
@@ -192,18 +146,9 @@
},
{
"cell_type": "code",
- "execution_count": 68,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "THIS IS A TEST STRING\n",
- "this is a test string\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"s = 'This is a Test String'\n",
"print(s.upper())\n",
@@ -219,17 +164,9 @@
},
{
"cell_type": "code",
- "execution_count": 69,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "This is a Better String\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"s = 'This is a Test String'\n",
"s2 = s.replace('Test', 'Better')\n",
@@ -245,17 +182,9 @@
},
{
"cell_type": "code",
- "execution_count": 70,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "This is an example of an example String\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"import re\n",
"s = 'This is a test of a Test String'\n",
@@ -277,17 +206,9 @@
},
{
"cell_type": "code",
- "execution_count": 71,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "['This', 'is', 'a', 'test', 'of', 'a', 'Test', 'String']\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(s.split())"
]
@@ -311,18 +232,9 @@
},
{
"cell_type": "code",
- "execution_count": 72,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "(3, 7.6, 'str')\n",
- "[1, 'mj', -5.4]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"xtuple = (3, 7.6, 'str')\n",
"xlist = [1, 'mj', -5.4]\n",
@@ -339,18 +251,9 @@
},
{
"cell_type": "code",
- "execution_count": 73,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "x2 is: ((3, 7.6, 'str'), [1, 'mj', -5.4])\n",
- "x3 is: [(3, 7.6, 'str'), [1, 'mj', -5.4]]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"x2 = (xtuple, xlist)\n",
"x3 = [xtuple, xlist]\n",
@@ -369,17 +272,9 @@
},
{
"cell_type": "code",
- "execution_count": 74,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30, 70, 80]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [10, 20, 30]\n",
"a = a + [70]\n",
@@ -398,17 +293,9 @@
},
{
"cell_type": "code",
- "execution_count": 75,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "20\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"d = [10, 20, 30]\n",
"print(d[1])"
@@ -424,18 +311,9 @@
},
{
"cell_type": "code",
- "execution_count": 76,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "10\n",
- "30\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [10, 20, 30, 40, 50, 60]\n",
"print(a[0])\n",
@@ -451,18 +329,9 @@
},
{
"cell_type": "code",
- "execution_count": 77,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "60\n",
- "10\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(a[-1])\n",
"print(a[-6])"
@@ -477,42 +346,18 @@
},
{
"cell_type": "code",
- "execution_count": 78,
- "metadata": {},
- "outputs": [
- {
- "ename": "IndexError",
- "evalue": "list index out of range",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-78-f4cf4536701c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m7\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m: list index out of range"
- ],
- "output_type": "error"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(a[-7])"
]
},
{
"cell_type": "code",
- "execution_count": 79,
- "metadata": {},
- "outputs": [
- {
- "ename": "IndexError",
- "evalue": "list index out of range",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-79-52d95fbe5286>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m6\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m: list index out of range"
- ],
- "output_type": "error"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(a[6])"
]
@@ -526,17 +371,9 @@
},
{
"cell_type": "code",
- "execution_count": 80,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "6\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(len(a))"
]
@@ -550,18 +387,9 @@
},
{
"cell_type": "code",
- "execution_count": 81,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "20\n",
- "40\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"b = [[10, 20, 30], [40, 50, 60]]\n",
"print(b[0][1])\n",
@@ -584,17 +412,9 @@
},
{
"cell_type": "code",
- "execution_count": 82,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print(a[0:3])"
]
@@ -611,18 +431,9 @@
},
{
"cell_type": "code",
- "execution_count": 83,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30]\n",
- "[20, 30]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [10, 20, 30, 40, 50, 60]\n",
"print(a[0:3]) # same as a(1:3) in MATLAB\n",
@@ -641,21 +452,9 @@
},
{
"cell_type": "code",
- "execution_count": 84,
- "metadata": {},
- "outputs": [
- {
- "ename": "TypeError",
- "evalue": "list indices must be integers or slices, not list",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-84-aad7915ae3d8>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mb\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m4\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mTypeError\u001b[0m: list indices must be integers or slices, not list"
- ],
- "output_type": "error"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"b = [3, 4]\n",
"print(a[b])"
@@ -672,17 +471,9 @@
},
{
"cell_type": "code",
- "execution_count": 85,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30, 10, 20, 30, 10, 20, 30, 10, 20, 30]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"d = [10, 20, 30]\n",
"print(d * 4)"
@@ -697,19 +488,9 @@
},
{
"cell_type": "code",
- "execution_count": 86,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[10, 20, 30, 40]\n",
- "[10, 30, 40]\n",
- "[30, 40]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"d.append(40)\n",
"print(d)\n",
@@ -728,19 +509,9 @@
},
{
"cell_type": "code",
- "execution_count": 87,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "10\n",
- "20\n",
- "30\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"d = [10, 20, 30]\n",
"for x in d:\n",
@@ -760,134 +531,9 @@
},
{
"cell_type": "code",
- "execution_count": 88,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Help on list object:\n",
- "\n",
- "class list(object)\n",
- " | list() -> new empty list\n",
- " | list(iterable) -> new list initialized from iterable's items\n",
- " | \n",
- " | Methods defined here:\n",
- " | \n",
- " | __add__(self, value, /)\n",
- " | Return self+value.\n",
- " | \n",
- " | __contains__(self, key, /)\n",
- " | Return key in self.\n",
- " | \n",
- " | __delitem__(self, key, /)\n",
- " | Delete self[key].\n",
- " | \n",
- " | __eq__(self, value, /)\n",
- " | Return self==value.\n",
- " | \n",
- " | __ge__(self, value, /)\n",
- " | Return self>=value.\n",
- " | \n",
- " | __getattribute__(self, name, /)\n",
- " | Return getattr(self, name).\n",
- " | \n",
- " | __getitem__(...)\n",
- " | x.__getitem__(y) <==> x[y]\n",
- " | \n",
- " | __gt__(self, value, /)\n",
- " | Return self>value.\n",
- " | \n",
- " | __iadd__(self, value, /)\n",
- " | Implement self+=value.\n",
- " | \n",
- " | __imul__(self, value, /)\n",
- " | Implement self*=value.\n",
- " | \n",
- " | __init__(self, /, *args, **kwargs)\n",
- " | Initialize self. See help(type(self)) for accurate signature.\n",
- " | \n",
- " | __iter__(self, /)\n",
- " | Implement iter(self).\n",
- " | \n",
- " | __le__(self, value, /)\n",
- " | Return self<=value.\n",
- " | \n",
- " | __len__(self, /)\n",
- " | Return len(self).\n",
- " | \n",
- " | __lt__(self, value, /)\n",
- " | Return self<value.\n",
- " | \n",
- " | __mul__(self, value, /)\n",
- " | Return self*value.n\n",
- " | \n",
- " | __ne__(self, value, /)\n",
- " | Return self!=value.\n",
- " | \n",
- " | __new__(*args, **kwargs) from builtins.type\n",
- " | Create and return a new object. See help(type) for accurate signature.\n",
- " | \n",
- " | __repr__(self, /)\n",
- " | Return repr(self).\n",
- " | \n",
- " | __reversed__(...)\n",
- " | L.__reversed__() -- return a reverse iterator over the list\n",
- " | \n",
- " | __rmul__(self, value, /)\n",
- " | Return self*value.\n",
- " | \n",
- " | __setitem__(self, key, value, /)\n",
- " | Set self[key] to value.\n",
- " | \n",
- " | __sizeof__(...)\n",
- " | L.__sizeof__() -- size of L in memory, in bytes\n",
- " | \n",
- " | append(...)\n",
- " | L.append(object) -> None -- append object to end\n",
- " | \n",
- " | clear(...)\n",
- " | L.clear() -> None -- remove all items from L\n",
- " | \n",
- " | copy(...)\n",
- " | L.copy() -> list -- a shallow copy of L\n",
- " | \n",
- " | count(...)\n",
- " | L.count(value) -> integer -- return number of occurrences of value\n",
- " | \n",
- " | extend(...)\n",
- " | L.extend(iterable) -> None -- extend list by appending elements from the iterable\n",
- " | \n",
- " | index(...)\n",
- " | L.index(value, [start, [stop]]) -> integer -- return first index of value.\n",
- " | Raises ValueError if the value is not present.\n",
- " | \n",
- " | insert(...)\n",
- " | L.insert(index, object) -- insert object before index\n",
- " | \n",
- " | pop(...)\n",
- " | L.pop([index]) -> item -- remove and return item at index (default last).\n",
- " | Raises IndexError if list is empty or index is out of range.\n",
- " | \n",
- " | remove(...)\n",
- " | L.remove(value) -> None -- remove first occurrence of value.\n",
- " | Raises ValueError if the value is not present.\n",
- " | \n",
- " | reverse(...)\n",
- " | L.reverse() -- reverse *IN PLACE*\n",
- " | \n",
- " | sort(...)\n",
- " | L.sort(key=None, reverse=False) -> None -- stable sort *IN PLACE*\n",
- " | \n",
- " | ----------------------------------------------------------------------\n",
- " | Data and other attributes defined here:\n",
- " | \n",
- " | __hash__ = None\n",
- "\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"help(d)"
]
@@ -901,64 +547,9 @@
},
{
"cell_type": "code",
- "execution_count": 89,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "['__add__',\n",
- " '__class__',\n",
- " '__contains__',\n",
- " '__delattr__',\n",
- " '__delitem__',\n",
- " '__dir__',\n",
- " '__doc__',\n",
- " '__eq__',\n",
- " '__format__',\n",
- " '__ge__',\n",
- " '__getattribute__',\n",
- " '__getitem__',\n",
- " '__gt__',\n",
- " '__hash__',\n",
- " '__iadd__',\n",
- " '__imul__',\n",
- " '__init__',\n",
- " '__iter__',\n",
- " '__le__',\n",
- " '__len__',\n",
- " '__lt__',\n",
- " '__mul__',\n",
- " '__ne__',\n",
- " '__new__',\n",
- " '__reduce__',\n",
- " '__reduce_ex__',\n",
- " '__repr__',\n",
- " '__reversed__',\n",
- " '__rmul__',\n",
- " '__setattr__',\n",
- " '__setitem__',\n",
- " '__sizeof__',\n",
- " '__str__',\n",
- " '__subclasshook__',\n",
- " 'append',\n",
- " 'clear',\n",
- " 'copy',\n",
- " 'count',\n",
- " 'extend',\n",
- " 'index',\n",
- " 'insert',\n",
- " 'pop',\n",
- " 'remove',\n",
- " 'reverse',\n",
- " 'sort']"
- ]
- },
- "execution_count": 89,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"dir(d)"
]
@@ -978,20 +569,9 @@
},
{
"cell_type": "code",
- "execution_count": 90,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "2\n",
- "dict_keys(['b', 'a'])\n",
- "dict_values([20, 10])\n",
- "10\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"e = {'a' : 10, 'b': 20}\n",
"print(len(e))\n",
@@ -1015,17 +595,9 @@
},
{
"cell_type": "code",
- "execution_count": 91,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{'c': 555, 'b': 20, 'a': 10}\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"e['c'] = 555 # just like in Biobank! ;)\n",
"print(e)"
@@ -1042,18 +614,9 @@
},
{
"cell_type": "code",
- "execution_count": 92,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{'c': 555, 'a': 10}\n",
- "{'a': 10}\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"e.pop('b')\n",
"print(e)\n",
@@ -1072,19 +635,9 @@
},
{
"cell_type": "code",
- "execution_count": 93,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "('c', 555)\n",
- "('b', 20)\n",
- "('a', 10)\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"e = {'a' : 10, 'b': 20, 'c':555}\n",
"for k, v in e.items():\n",
@@ -1102,19 +655,9 @@
},
{
"cell_type": "code",
- "execution_count": 94,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "('c', 555)\n",
- "('b', 20)\n",
- "('a', 10)\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"for k in e:\n",
" print((k, e[k]))"
@@ -1137,17 +680,9 @@
},
{
"cell_type": "code",
- "execution_count": 95,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "7\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = 7\n",
"b = a\n",
@@ -1164,17 +699,9 @@
},
{
"cell_type": "code",
- "execution_count": 96,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[8888]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [7]\n",
"b = a\n",
@@ -1191,17 +718,9 @@
},
{
"cell_type": "code",
- "execution_count": 97,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[7, 7]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [7]\n",
"b = a * 2\n",
@@ -1218,17 +737,9 @@
},
{
"cell_type": "code",
- "execution_count": 98,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[7]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [7]\n",
"b = list(a)\n",
@@ -1245,18 +756,9 @@
},
{
"cell_type": "code",
- "execution_count": 99,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "(2, 5, 7)\n",
- "[2, 5, 7]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"xt = (2, 5, 7)\n",
"xl = list(xt)\n",
@@ -1275,20 +777,9 @@
},
{
"cell_type": "code",
- "execution_count": 100,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[5]\n",
- "[5, 10]\n",
- "[5, 10]\n",
- "[5, 10]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"def foo1(x):\n",
" x.append(10)\n",
@@ -1326,21 +817,9 @@
},
{
"cell_type": "code",
- "execution_count": 101,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Not a is: False\n",
- "Not 1 is: False\n",
- "Not 0 is: True\n",
- "Not {} is: True\n",
- "{}==0 is: False\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = True\n",
"print('Not a is:', not a)\n",
@@ -1359,19 +838,9 @@
},
{
"cell_type": "code",
- "execution_count": 102,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "False\n",
- "True\n",
- "True\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"print('the' in 'a number of words')\n",
"print('of' in 'a number of words')\n",
@@ -1389,18 +858,9 @@
},
{
"cell_type": "code",
- "execution_count": 103,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "0.9933407850276534\n",
- "Positive\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"import random\n",
"a = random.uniform(-1, 1)\n",
@@ -1422,17 +882,9 @@
},
{
"cell_type": "code",
- "execution_count": 104,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Variable is true, or at least not empty\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"a = [] # just one of many examples\n",
"if not a:\n",
@@ -1454,21 +906,9 @@
},
{
"cell_type": "code",
- "execution_count": 105,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "2\n",
- "is\n",
- "more\n",
- "than\n",
- "1\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"for x in [2, 'is', 'more', 'than', 1]:\n",
" print(x)"
@@ -1485,23 +925,9 @@
},
{
"cell_type": "code",
- "execution_count": 106,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "2\n",
- "3\n",
- "4\n",
- "5\n",
- "6\n",
- "7\n",
- "8\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"for x in range(2, 9):\n",
" print(x)"
@@ -1518,18 +944,9 @@
},
{
"cell_type": "code",
- "execution_count": 107,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "4\n",
- "7\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"x, y = [4, 7]\n",
"print(x)\n",
@@ -1545,21 +962,9 @@
},
{
"cell_type": "code",
- "execution_count": 108,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[('Some', 0), ('set', 1), ('of', 2), ('items', 3)]\n",
- "0 Some\n",
- "1 set\n",
- "2 of\n",
- "3 items\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"alist = ['Some', 'set', 'of', 'items']\n",
"blist = list(range(len(alist)))\n",
@@ -1581,17 +986,9 @@
},
{
"cell_type": "code",
- "execution_count": 109,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "35.041627991396396\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"import random\n",
"n = 0\n",
@@ -1625,17 +1022,9 @@
},
{
"cell_type": "code",
- "execution_count": 110,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "0.6576892259376057 0.11717666603919556\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"import random\n",
"x = random.uniform(0, 1)\n",
@@ -1654,18 +1043,9 @@
},
{
"cell_type": "code",
- "execution_count": 111,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[0, 1, 4, 9, 16, 25, 36, 49, 64, 81]\n",
- "[0, 1, 4, 9, 16, 25, 36, 64, 81]\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"v1 = [ x**2 for x in range(10) ]\n",
"print(v1)\n",
@@ -1679,34 +1059,9 @@
"source": [
"You'll find that python programmers use this kind of construction _*a lot*_."
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
}
],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.5.2"
- }
- },
+ "metadata": {},
"nbformat": 4,
"nbformat_minor": 2
}
diff --git a/getting_started/basics.md b/getting_started/01_basics.md
similarity index 100%
rename from getting_started/basics.md
rename to getting_started/01_basics.md
diff --git a/getting_started/nifti.ipynb b/getting_started/05_nifti.ipynb
similarity index 78%
rename from getting_started/nifti.ipynb
rename to getting_started/05_nifti.ipynb
index 994edd80c08830bcf5e2d0ab2bb116f1ac5f4029..f157ec0113f48fb0a2d900017b926ed1db17116d 100644
--- a/getting_started/nifti.ipynb
+++ b/getting_started/05_nifti.ipynb
@@ -15,17 +15,9 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "(182, 218, 182)\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"import numpy as np\n",
"import nibabel as nib\n",
@@ -65,17 +57,9 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "(1.0, 1.0, 1.0)\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"voxsize = imhdr.get_zooms()\n",
"print(voxsize)"
@@ -92,21 +76,9 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "4\n",
- "[[ -1. 0. 0. 90.]\n",
- " [ 0. 1. 0. -126.]\n",
- " [ 0. 0. 1. -72.]\n",
- " [ 0. 0. 0. 1.]]\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"sform = imhdr.get_sform()\n",
"sformcode = imhdr['sform_code']\n",
@@ -127,7 +99,7 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -147,25 +119,7 @@
]
}
],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.5.2"
- }
- },
+ "metadata": {},
"nbformat": 4,
"nbformat_minor": 2
}
diff --git a/getting_started/nifti.md b/getting_started/05_nifti.md
similarity index 100%
rename from getting_started/nifti.md
rename to getting_started/05_nifti.md
diff --git a/getting_started/scripts.ipynb b/getting_started/08_scripts.ipynb
similarity index 63%
rename from getting_started/scripts.ipynb
rename to getting_started/08_scripts.ipynb
index 7b87ec6388573c9cebb864bdbea98da654593e9c..1d3d705d5b636c281ce97e6a527431c69075847d 100644
--- a/getting_started/scripts.ipynb
+++ b/getting_started/08_scripts.ipynb
@@ -18,9 +18,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"#!/usr/bin/env python"
@@ -38,9 +36,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"#!/usr/bin/env fslpython"
@@ -60,9 +56,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import subprocess as sp\n",
@@ -79,9 +73,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"spobj = sp.run(['ls'], stdout = sp.PIPE)"
@@ -97,9 +89,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"spobj = sp.run('ls -la'.split(), stdout = sp.PIPE)\n",
@@ -119,9 +109,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import os\n",
@@ -143,9 +131,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"commands = \"\"\"\n",
@@ -176,9 +162,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"import sys\n",
@@ -200,19 +184,10 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Usage: bash <input image> <output image>\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "%%bash\n",
"#!/bin/bash\n",
"if [ $# -lt 2 ] ; then\n",
" echo \"Usage: $0 <input image> <output image>\"\n",
@@ -238,21 +213,9 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "ename": "IndexError",
- "evalue": "list index out of range",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-2-f7378930c369>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0mspobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfsldir\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m'/bin/fslstats'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'-V'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstdout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPIPE\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0msout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 15\u001b[0;31m \u001b[0mvol_vox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 16\u001b[0m \u001b[0mvol_mm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Volumes are: '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_vox\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in voxels and '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_mm\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in mm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;31mIndexError\u001b[0m: list index out of range"
- ],
- "output_type": "error"
- }
- ],
+ "outputs": [],
"source": [
"#!/usr/bin/env fslpython\n",
"import os, sys\n",
@@ -272,55 +235,9 @@
"vol_mm = float(sout.split()[1])\n",
"print('Volumes are: ', vol_vox, ' in voxels and ', vol_mm, ' in mm')"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": []
}
],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.2"
- },
- "toc": {
- "colors": {
- "hover_highlight": "#DAA520",
- "running_highlight": "#FF0000",
- "selected_highlight": "#FFD700"
- },
- "moveMenuLeft": true,
- "nav_menu": {
- "height": "105px",
- "width": "252px"
- },
- "navigate_menu": true,
- "number_sections": true,
- "sideBar": true,
- "threshold": 4.0,
- "toc_cell": false,
- "toc_section_display": "block",
- "toc_window_display": false
- }
- },
+ "metadata": {},
"nbformat": 4,
"nbformat_minor": 2
}
diff --git a/getting_started/scripts.md b/getting_started/08_scripts.md
similarity index 100%
rename from getting_started/scripts.md
rename to getting_started/08_scripts.md