From e93a51e1b7f345edfee779569b27ccb951ba790f Mon Sep 17 00:00:00 2001
From: Tamas Gal <tgal@km3net.de>
Date: Wed, 4 Mar 2020 14:03:45 +0100
Subject: [PATCH] Remove obselete Reader class
---
km3io/offline.py | 65 -----
notebooks/Reader_tutorial.ipynb | 440 --------------------------------
tests/test_offline.py | 68 +----
3 files changed, 1 insertion(+), 572 deletions(-)
delete mode 100644 notebooks/Reader_tutorial.ipynb
diff --git a/km3io/offline.py b/km3io/offline.py
index e9c4ead..862ffc9 100644
--- a/km3io/offline.py
+++ b/km3io/offline.py
@@ -211,71 +211,6 @@ class OfflineKeys:
return km3io.definitions.trigger.data
-class Reader:
- """Reader for one offline ROOT file"""
- def __init__(self, file_path):
- """ Reader class is an offline ROOT file reader. This class is a
- "very" low level I/O.
-
- Parameters
- ----------
- file_path : str or file-like object
- The file of interest.
- """
- self._tree = uproot.open(file_path)[MAIN_TREE_NAME]
- self._data = self._tree.lazyarrays(
- basketcache=uproot.cache.ThreadSafeArrayCache(BASKET_CACHE_SIZE))
- self._keys = None
-
- def __getitem__(self, key):
- """reads data stored in the branch of interest in an Evt 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>`
- .
-
- Raises
- ------
- KeyError
- Some branches in an offline file structure are "fake branches" and
- do not contain data. Therefore, the keys corresponding to these
- fake branches are not read.
- """
- keys = self.keys.valid_keys
- if key not in keys and not isinstance(key, int):
- raise KeyError(
- "'{}' is not a valid key or is a fake branch.".format(key))
- return self._data[key]
-
- def __len__(self):
- return len(self._data)
-
- def __repr__(self):
- return "<{}: {} entries>".format(self.__class__.__name__, len(self))
-
- @cached_property
- def keys(self):
- """wrapper for all keys in an offline file.
-
- Returns
- -------
- Class
- OfflineKeys.
- """
- return OfflineKeys(self._tree)
-
-
class OfflineReader:
"""reader for offline ROOT files"""
def __init__(self, file_path=None):
diff --git a/notebooks/Reader_tutorial.ipynb b/notebooks/Reader_tutorial.ipynb
deleted file mode 100644
index 808e545..0000000
--- a/notebooks/Reader_tutorial.ipynb
+++ /dev/null
@@ -1,440 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "['/home/zineb/km3net/km3net/km3io/notebooks', '/home/zineb/miniconda3/envs/km3pipe/lib/python37.zip', '/home/zineb/miniconda3/envs/km3pipe/lib/python3.7', '/home/zineb/miniconda3/envs/km3pipe/lib/python3.7/lib-dynload', '', '/home/zineb/miniconda3/envs/km3pipe/lib/python3.7/site-packages', '/home/zineb/km3net/km3net/km3io', '/home/zineb/miniconda3/envs/km3pipe/lib/python3.7/site-packages/IPython/extensions', '/home/zineb/.ipython', '/home/zineb/km3net/km3net/km3io']\n"
- ]
- }
- ],
- "source": [
- "# Add file to current python path\n",
- "from pathlib import Path\n",
- "import sys\n",
- "sys.path.append(str(Path.cwd().parent))\n",
- "Path.cwd()\n",
- "print(sys.path)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {},
- "outputs": [],
- "source": [
- "from km3io.aanet import Reader"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {},
- "outputs": [],
- "source": [
- "# test samples directory - aanet test file\n",
- "files_path = Path.cwd().parent / 'tests/samples' \n",
- "aanet_file = files_path / 'aanet_v2.0.0.root'"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "metadata": {
- "scrolled": true
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "<Reader: 10 entries>"
- ]
- },
- "execution_count": 4,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "reader = Reader(aanet_file)\n",
- "reader"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "['trks.fUniqueID',\n",
- " 'trks.fBits',\n",
- " 'trks.id',\n",
- " 'trks.pos.x',\n",
- " 'trks.pos.y',\n",
- " 'trks.pos.z',\n",
- " 'trks.dir.x',\n",
- " 'trks.dir.y',\n",
- " 'trks.dir.z',\n",
- " 'trks.t',\n",
- " 'trks.E',\n",
- " 'trks.len',\n",
- " 'trks.lik',\n",
- " 'trks.type',\n",
- " 'trks.rec_type',\n",
- " 'trks.rec_stages',\n",
- " 'trks.status',\n",
- " 'trks.mother_id',\n",
- " 'trks.fitinf',\n",
- " 'trks.hit_ids',\n",
- " 'trks.error_matrix',\n",
- " 'trks.comment']"
- ]
- },
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "reader.keys.tracks_keys"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "<Table [<Row 0> <Row 1> <Row 2> ... <Row 7> <Row 8> <Row 9>] at 0x7fed2d98a750>"
- ]
- },
- "execution_count": 6,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# big lazyarray with ALL file data!\n",
- "lazy_data = reader._data\n",
- "lazy_data"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "<ChunkedArray [5971 5971 5971 ... 5971 5971 5971] at 0x7fed2d91f9d0>"
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# getting the run_id for a specific event (event 5 for example)\n",
- "reader['run_id']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "60"
- ]
- },
- "execution_count": 8,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# one can check how many hits are in event 5\n",
- "reader[5]['hits']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "56"
- ]
- },
- "execution_count": 9,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# one can also check how many tracks are in event 5\n",
- "reader[5]['trks']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 10,
- "metadata": {},
- "outputs": [],
- "source": [
- "# # the user is reminded to always specify the \"correct\" event/hits/tracks \n",
- "# # key in the Aanet event file\n",
- "# try:\n",
- "# reader['whatever']\n",
- "# except KeyError as e:\n",
- "# print(e)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Now let's explore in more details the hits:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 11,
- "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 0x7fed2d8af450>"
- ]
- },
- "execution_count": 11,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# reading all data from a specific branch in hits data: for example \n",
- "# 'hits.dom_id'\n",
- "reader['hits.dom_id']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 12,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "array([806455814, 806487219, 806487219, 806487219, 806487226, 808432835,\n",
- " 808432835, 808432835, 808432835, 808432835, 808432835, 808432835,\n",
- " 808451904, 808451904, 808451907, 808451907, 808469129, 808469129,\n",
- " 808469129, 808493910, 808949744, 808949744, 808951460, 808951460,\n",
- " 808956908, 808961655, 808964908, 808969848, 808969857, 808972593,\n",
- " 808972593, 808972598, 808972598, 808972698, 808972698, 808974758,\n",
- " 808974811, 808976377, 808981510, 808981523, 808981812, 808982005,\n",
- " 808982005, 808982018, 808982077, 808982077, 808982547, 809007627,\n",
- " 809521500, 809521500, 809521500, 809524432, 809526097, 809526097,\n",
- " 809526097, 809526097, 809526097, 809526097, 809526097, 809544058],\n",
- " dtype=int32)"
- ]
- },
- "execution_count": 12,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# the user can access hits.dom_id data for a specific event (for example \n",
- "# event 5)\n",
- "reader['hits.dom_id'][5]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 13,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "60"
- ]
- },
- "execution_count": 13,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# We previsouly checked (using reader[5]['hits']) that event\n",
- "# 5 has 60 hits, now we can see that reader['hits.dom_id'][5]\n",
- "# has exaclty 60 dom ids as well! \n",
- "len(reader['hits.dom_id'][5])"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 14,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "806455814"
- ]
- },
- "execution_count": 14,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# one can access a dom id of the first hit \n",
- "reader['hits.dom_id'][5][0]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Now let's explore in more details the tracks:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 15,
- "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 0x7fed2d8b8850>"
- ]
- },
- "execution_count": 15,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# reading all data from a specific branch in tracks data:\n",
- "reader['trks.dir.z']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 16,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "array([-0.60246049, -0.60246049, -0.60246049, -0.51420541, -0.5475772 ,\n",
- " -0.5772408 , -0.56068238, -0.64907684, -0.67781799, -0.66565114,\n",
- " -0.63014839, -0.64566464, -0.62691012, -0.58465493, -0.59287533,\n",
- " -0.63655091, -0.63771247, -0.73446841, -0.7456636 , -0.70941246,\n",
- " -0.66312268, -0.66312268, -0.56806477, -0.56806477, -0.66312268,\n",
- " -0.66312268, -0.74851077, -0.74851077, -0.66312268, -0.74851077,\n",
- " -0.56806477, -0.74851077, -0.66312268, -0.74851077, -0.56806477,\n",
- " -0.66312268, -0.56806477, -0.66312268, -0.56806477, -0.56806477,\n",
- " -0.66312268, -0.74851077, -0.66312268, -0.93501626, -0.56806477,\n",
- " -0.74851077, -0.66312268, -0.56806477, -0.82298389, -0.74851077,\n",
- " -0.66312268, -0.56806477, -0.82298389, -0.56806477, -0.66312268,\n",
- " -0.97094183])"
- ]
- },
- "execution_count": 16,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# the user can access trks.dir.z data for a specific event (for example \n",
- "# event 5)\n",
- "reader['trks.dir.z'][5]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 17,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "56"
- ]
- },
- "execution_count": 17,
- "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['trks.dir.z'][5]\n",
- "# has exaclty 56 values of trks.dir.z as well! \n",
- "len(reader['trks.dir.z'][5])"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 18,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "-0.6024604933159441"
- ]
- },
- "execution_count": 18,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# one can access the first trks.dir.z from event 5 using \n",
- "reader['trks.dir.z'][5][0]"
- ]
- }
- ],
- "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": "3.7.4"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/tests/test_offline.py b/tests/test_offline.py
index 0fa6eff..60ae196 100644
--- a/tests/test_offline.py
+++ b/tests/test_offline.py
@@ -2,7 +2,7 @@ import unittest
import numpy as np
from pathlib import Path
-from km3io.offline import Reader, OfflineEvents, OfflineHits, OfflineTracks
+from km3io.offline import OfflineEvents, OfflineHits, OfflineTracks
from km3io import OfflineReader
SAMPLES_DIR = Path(__file__).parent / 'samples'
@@ -42,72 +42,6 @@ class TestOfflineKeys(unittest.TestCase):
self.assertEqual(len(self.keys.fit_keys), 18)
-class TestReader(unittest.TestCase):
- def setUp(self):
- self.r = Reader(OFFLINE_FILE)
- self.lengths = {0: 176, 1: 125, -1: 105}
- self.total_item_count = 1434
-
- def test_reading_dom_id(self):
- dom_ids = self.r["hits.dom_id"]
-
- for event_id, length in self.lengths.items():
- self.assertEqual(length, len(dom_ids[event_id]))
-
- self.assertEqual(self.total_item_count, sum(dom_ids.count()))
-
- self.assertListEqual([806451572, 806451572, 806451572],
- list(dom_ids[0][:3]))
-
- def test_reading_channel_id(self):
- channel_ids = self.r["hits.channel_id"]
-
- for event_id, length in self.lengths.items():
- self.assertEqual(length, len(channel_ids[event_id]))
-
- self.assertEqual(self.total_item_count, sum(channel_ids.count()))
-
- self.assertListEqual([8, 9, 14], list(channel_ids[0][:3]))
-
- # channel IDs are always between [0, 30]
- self.assertTrue(all(c >= 0 for c in channel_ids.min()))
- self.assertTrue(all(c < 31 for c in channel_ids.max()))
-
- def test_reading_times(self):
- ts = self.r["hits.t"]
-
- for event_id, length in self.lengths.items():
- self.assertEqual(length, len(ts[event_id]))
-
- self.assertEqual(self.total_item_count, sum(ts.count()))
-
- self.assertListEqual([70104010.0, 70104016.0, 70104192.0],
- list(ts[0][:3]))
-
- def test_reading_keys(self):
- # there are 106 "valid" keys in an offline file
- self.assertEqual(len(self.r.keys.valid_keys), 106)
-
- # there are 20 hits keys
- self.assertEqual(len(self.r.keys.hits_keys), 20)
- self.assertEqual(len(self.r.keys.mc_hits_keys), 20)
-
- # there are 22 tracks keys
- self.assertEqual(len(self.r.keys.tracks_keys), 22)
- self.assertEqual(len(self.r.keys.mc_tracks_keys), 22)
-
- def test_raising_KeyError(self):
- # non valid keys must raise a KeyError
- with self.assertRaises(KeyError):
- self.r['whatever']
-
- def test_number_events(self):
- Nevents = len(self.r)
-
- # check that there are 10 events
- self.assertEqual(Nevents, 10)
-
-
class TestOfflineReader(unittest.TestCase):
def setUp(self):
self.r = OfflineReader(OFFLINE_FILE)
--
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