From e7eb425b8f4b24006186019317b58f41282a6420 Mon Sep 17 00:00:00 2001
From: zineb aly <aly.zineb.az@gmail.com>
Date: Sun, 17 Nov 2019 20:19:08 +0100
Subject: [PATCH] adapted AanetReader format to pep8
---
km3io/aanet.py | 62 ++++++----
notebooks/AanetReader_tutorial.ipynb | 162 +++++++++------------------
2 files changed, 90 insertions(+), 134 deletions(-)
diff --git a/km3io/aanet.py b/km3io/aanet.py
index 6a3b161..247ecbd 100644
--- a/km3io/aanet.py
+++ b/km3io/aanet.py
@@ -1,15 +1,16 @@
import uproot
+
class AanetReader:
"""Reader for one Aanet ROOT file"""
def __init__(self, file_path):
""" AanetReader class is a Aanet ROOT file wrapper
-
+
Parameters
----------
file_path : path-like object
- Path to the file of interest. It can be a str or any python path-like object that points
- to the file of ineterst.
+ Path to the file of interest. It can be a str or any python
+ path-like object that points to the file of ineterst.
"""
self.file_path = file_path
self.data = uproot.open(self.file_path)['E']
@@ -18,52 +19,65 @@ class AanetReader:
self._hits_keys = None
self._tracks_keys = None
-
def __getitem__(self, key):
- """reads data stored in the branch of interest in an event tree.
-
+ """reads data stored in the branch of interest in an event tree.
+
Parameters
----------
key : str
name of the branch of interest in event data.
-
+
Returns
-------
lazyarray
- Lazyarray of all data stored in the branch of interest. A lazyarray is an array-like
- object that reads data on demand. Here, only the first and last chunks of data are
- read in memory, and not all data in the array. The output can be used
- with all `Numpy's universal functions <https://docs.scipy.org/doc/numpy/reference/ufuncs.html>`.
-
+ Lazyarray of all data stored in the branch of interest. A lazyarray
+ is an array-like object that reads data on demand. Here, only the
+ first and last chunks of data are read in memory, and not all data
+ in the array. The output can be used with all `Numpy's universal
+ functions <https://docs.scipy.org/doc/numpy/reference/ufuncs.html>`
+ .
+
Raises
------
KeyEroor
- Some branches in an Aanet file structure are "fake branches" and do not contain data. Therefore,
- the keys corresponding to these fake branches are not read.
+ Some branches in an Aanet file structure are "fake branches" and do
+ not contain data. Therefore, the keys corresponding to these fake
+ branches are not read.
"""
if key not in self.keys() and not isinstance(key, int):
raise KeyError(f"'{key}' is not a valid key or is a fake branch.")
return self.lazy_data[key]
def __len__(self):
-
return len(self.lazy_data)
def __repr__(self):
- return '\n'.join([f"Number of events: {self.__len__()}",
- "Events keys are:\n\t" + '\n\t'.join(self.events_keys),
- "Hits keys are:\n\t" + '\n\t'.join(self.hits_keys),
- "Tracks keys are:\n\t" + '\n\t'.join(self.tracks_keys)])
+ return '\n'.join([
+ f"Number of events: {self.__len__()}",
+ "Events keys are:\n\t" + '\n\t'.join(self.events_keys),
+ "Hits keys are:\n\t" + '\n\t'.join(self.hits_keys),
+ "Tracks keys are:\n\t" + '\n\t'.join(self.tracks_keys)
+ ])
def keys(self):
- return self.events_keys + self.hits_keys + self.tracks_keys
+ """constructs a list of all valid keys to be read from an Aanet event file.
+
+ Returns
+ -------
+ list
+ list of all valid keys.
+ """
+ return self.events_keys + self.hits_keys + self.tracks_keys
@property
def events_keys(self):
if self._events_keys is None:
- fake_branches = ['Evt', 'AAObject', 'TObject','t']
+ fake_branches = ['Evt', 'AAObject', 'TObject', 't']
t_baskets = ['t.fSec', 't.fNanoSec']
- self._events_keys = [key.decode('utf-8') for key in self.data['Evt'].keys() if key.decode('utf-8') not in fake_branches] + t_baskets
+ self._events_keys = [
+ key.decode('utf-8') for key in self.data['Evt'].keys()
+ if key.decode('utf-8') not in fake_branches
+ ] + t_baskets
return self._events_keys
@property
@@ -77,5 +91,7 @@ class AanetReader:
def tracks_keys(self):
if self._tracks_keys is None:
tracks_tree = self.data['Evt']['trks']
- self._tracks_keys = [key.decode('utf8') for key in tracks_tree.keys()]
+ self._tracks_keys = [
+ key.decode('utf8') for key in tracks_tree.keys()
+ ]
return self._tracks_keys
diff --git a/notebooks/AanetReader_tutorial.ipynb b/notebooks/AanetReader_tutorial.ipynb
index 5f4e757..4f79101 100644
--- a/notebooks/AanetReader_tutorial.ipynb
+++ b/notebooks/AanetReader_tutorial.ipynb
@@ -140,7 +140,7 @@
{
"data": {
"text/plain": [
- "<Table [<Row 0> <Row 1> <Row 2> ... <Row 7> <Row 8> <Row 9>] at 0x7f57ac134810>"
+ "<Table [<Row 0> <Row 1> <Row 2> ... <Row 7> <Row 8> <Row 9>] at 0x7f9011f02b50>"
]
},
"execution_count": 5,
@@ -156,7 +156,7 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -165,7 +165,7 @@
"5971"
]
},
- "execution_count": 11,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@@ -177,7 +177,7 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
@@ -186,7 +186,7 @@
"60"
]
},
- "execution_count": 12,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -198,7 +198,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -207,7 +207,7 @@
"56"
]
},
- "execution_count": 13,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
@@ -219,7 +219,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
@@ -248,16 +248,16 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "<ChunkedArray [[806451572 806451572 806451572 ... 809544061 809544061 809544061] [806451572 806451572 806451572 ... 809524432 809526097 809544061] [806451572 806451572 806451572 ... 809544061 809544061 809544061] ... [806451572 806455814 806465101 ... 809526097 809544058 809544061] [806455814 806455814 806455814 ... 809544061 809544061 809544061] [806455814 806455814 806455814 ... 809544058 809544058 809544061]] at 0x7f57997ee990>"
+ "<ChunkedArray [[806451572 806451572 806451572 ... 809544061 809544061 809544061] [806451572 806451572 806451572 ... 809524432 809526097 809544061] [806451572 806451572 806451572 ... 809544061 809544061 809544061] ... [806451572 806455814 806465101 ... 809526097 809544058 809544061] [806455814 806455814 806455814 ... 809544061 809544061 809544061] [806455814 806455814 806455814 ... 809544058 809544058 809544061]] at 0x7f9011eb3b10>"
]
},
- "execution_count": 15,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
@@ -270,7 +270,7 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
@@ -289,7 +289,7 @@
" dtype=int32)"
]
},
- "execution_count": 16,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
@@ -302,7 +302,7 @@
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 12,
"metadata": {},
"outputs": [
{
@@ -311,7 +311,7 @@
"60"
]
},
- "execution_count": 17,
+ "execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
@@ -325,7 +325,7 @@
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 13,
"metadata": {},
"outputs": [
{
@@ -334,7 +334,7 @@
"806455814"
]
},
- "execution_count": 20,
+ "execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
@@ -353,16 +353,16 @@
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "<ChunkedArray [[-0.872885221293917 -0.872885221293917 -0.872885221293917 ... -0.6631226836266504 -0.5680647731737454 -0.5680647731737454] [-0.8351996698137462 -0.8351996698137462 -0.8351996698137462 ... -0.7485107718446855 -0.8229838871876581 -0.239315690284641] [-0.989148723802379 -0.989148723802379 -0.989148723802379 ... -0.9350162572437829 -0.88545604390297 -0.88545604390297] ... [-0.5704611045902105 -0.5704611045902105 -0.5704611045902105 ... -0.9350162572437829 -0.4647231989130516 -0.4647231989130516] [-0.9779941383490359 -0.9779941383490359 -0.9779941383490359 ... -0.88545604390297 -0.88545604390297 -0.8229838871876581] [-0.7396916780974963 -0.7396916780974963 -0.7396916780974963 ... -0.6631226836266504 -0.7485107718446855 -0.7485107718446855]] at 0x7f57997f8d90>"
+ "<ChunkedArray [[-0.872885221293917 -0.872885221293917 -0.872885221293917 ... -0.6631226836266504 -0.5680647731737454 -0.5680647731737454] [-0.8351996698137462 -0.8351996698137462 -0.8351996698137462 ... -0.7485107718446855 -0.8229838871876581 -0.239315690284641] [-0.989148723802379 -0.989148723802379 -0.989148723802379 ... -0.9350162572437829 -0.88545604390297 -0.88545604390297] ... [-0.5704611045902105 -0.5704611045902105 -0.5704611045902105 ... -0.9350162572437829 -0.4647231989130516 -0.4647231989130516] [-0.9779941383490359 -0.9779941383490359 -0.9779941383490359 ... -0.88545604390297 -0.88545604390297 -0.8229838871876581] [-0.7396916780974963 -0.7396916780974963 -0.7396916780974963 ... -0.6631226836266504 -0.7485107718446855 -0.7485107718446855]] at 0x7f9011ebdf10>"
]
},
- "execution_count": 24,
+ "execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
@@ -374,7 +374,7 @@
},
{
"cell_type": "code",
- "execution_count": 25,
+ "execution_count": 15,
"metadata": {},
"outputs": [
{
@@ -394,7 +394,7 @@
" -0.97094183])"
]
},
- "execution_count": 25,
+ "execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
@@ -407,107 +407,47 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 16,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "56"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"# We previsouly checked (using reader[5]['trks']) that event\n",
- "# 5 has 56 tracks, now we can see that reader.hits_reader('hits.dom_id')[5]\n",
+ "# 5 has 56 tracks, now we can see that reader['trks.dir.z'][5]\n",
"# has exaclty 56 values of trks.dir.z as well! \n",
- "len(reader.read_tracks('trks.dir.z')[5])"
+ "len(reader['trks.dir.z'][5])"
]
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 17,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "-0.6024604933159441"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"# one can access the first trks.dir.z from event 5 using \n",
- "reader.read_tracks('trks.dir.z')[5][0]"
+ "reader['trks.dir.z'][5][0]"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# once again, the user is reminded to always use the tracks keys stored in Aanet\n",
- "# event file\n",
- "try:\n",
- " reader.read_tracks('whatever')\n",
- "except KeyError as e:\n",
- " print(e)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "reader['trks.dir.z']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "import numpy as np\n",
- "np.array(reader[0])"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
--
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