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[feat] add tracking.txt load class
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‎.github/workflows/linux_tests.yml‎

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name: Linux tests
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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linux:
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name: Linux Py${{ matrix.PYTHON_VERSION }}
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runs-on: ubuntu-latest
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env:
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CI: True
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PYTHON_VERSION: ${{ matrix.PYTHON_VERSION }}
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RUNNER_OS: 'ubuntu'
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strategy:
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fail-fast: false
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matrix:
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PYTHON_VERSION: ['3.6', '3.7', '3.8']
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steps:
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- name: Checkout branch
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uses: actions/checkout@v2
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- name: Install Conda
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uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: test
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auto-update-conda: true
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auto-activate-base: false
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python-version: ${{ matrix.PYTHON_VERSION }}
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- name: Install package dependencies
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shell: bash -l {0}
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run: conda install --file requirements/conda.txt -y -q
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- name: Install test dependencies
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shell: bash -l {0}
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run: |
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conda install --file requirements/tests.txt -y -q
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- name: Run tests
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shell: bash -l {0}
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run: |
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cd FastAnalysis/
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pytest tests/test_load.py

‎.github/workflows/macos_tests.yml‎

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name: Macos tests
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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macos:
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name: Mac Py${{ matrix.PYTHON_VERSION }}
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runs-on: macos-latest
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env:
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CI: True
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PYTHON_VERSION: ${{ matrix.PYTHON_VERSION }}
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RUNNER_OS: 'macos'
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strategy:
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fail-fast: false
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matrix:
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PYTHON_VERSION: ['3.6', '3.7', '3.8']
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steps:
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- name: Checkout branch
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uses: actions/checkout@v2
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- name: Install Conda
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uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: test
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auto-update-conda: true
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auto-activate-base: false
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python-version: ${{ matrix.PYTHON_VERSION }}
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- name: Install package dependencies
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shell: bash -l {0}
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run: conda install --file requirements/conda.txt -y -q
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- name: Install test dependencies
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shell: bash -l {0}
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run: |
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conda install --file requirements/tests.txt -y -q
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- name: Run tests
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shell: bash -l {0}
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run: |
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cd FastAnalysis/
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pytest tests/test_load.py

‎.github/workflows/win_tests.yml‎

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name: Windows tests
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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windows:
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name: Windows Py${{ matrix.PYTHON_VERSION }}
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runs-on: windows-latest
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env:
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CI: True
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PYTHON_VERSION: ${{ matrix.PYTHON_VERSION }}
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RUNNER_OS: 'windows'
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strategy:
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fail-fast: false
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matrix:
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PYTHON_VERSION: ['3.6', '3.7', '3.8']
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steps:
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- name: Checkout branch
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uses: actions/checkout@v2
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- name: Install Conda
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uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: test
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auto-update-conda: true
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auto-activate-base: false
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python-version: ${{ matrix.PYTHON_VERSION }}
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- name: Install package dependencies
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shell: bash -l {0}
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run: conda install --file requirements/conda.txt -y -q
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- name: Install test dependencies
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shell: bash -l {0}
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run: |
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conda install --file requirements/tests.txt -y -q
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- name: Run tests
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shell: bash -l {0}
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run: |
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cd FastAnalysis/
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pytest tests/test_load.py

‎FastAnalysis/load.py‎

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import pandas
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import os
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class Load:
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"""Base class to load tracking.txt files"""
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def __init__(self, path):
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"""
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Constructor for Load.
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:param [path]: [Path to the tracking.txt file.]
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:type [path]: [str]
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...
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:raises [Exception]: []
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"""
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self.path = os.path.abspath(path)
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try:
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self.tracking = pandas.read_csv(path, sep='\t')
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except Exception as e:
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raise e
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def getDataframe(self):
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"""
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Get the tracking data in a DataFrame.
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:raises [Exception]: [The selected file is empty]
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...
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:return: [Tracking data]
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:rtype: [DataFrame]
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"""
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if self.tracking.empty:
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raise Exception("The selected file is empty")
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else:
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return self.tracking
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def getObjectNumber(self):
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"""
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Get the total number of objects.
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...
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:return: [Total number of objects]
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:rtype: [int]
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"""
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maxObj = len(set(self.tracking.id.values))
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return maxObj
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def getObject(self, iD):
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"""
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Get the data for the object with id.
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:param [iD]: [Id of the object.]
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:type [index]: [int]
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...
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:return: [Data for the object id.]
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:rtype: [DataFrame]
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"""
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objectData = self.tracking[self.tracking.id == iD]
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return objectData
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def getFrame(self, index):
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"""
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Get the data for the image number index.
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:param [index]: [Index of the image.]
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:type [index]: [int]
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...
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:return: [Data for the image index.]
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:rtype: [DataFrame]
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"""
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objectData = self.tracking[self.tracking.imageNumber == index]
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return objectData
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def getObjectInFrame(self, iD, index):
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"""
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Get the data for an object id is in a frame index.
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:param [iD]: [Id of the object.]
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:type [index]: [int]
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:param [index]: [Index of the image.]
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:type [index]: [int]
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...
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:return: [True if object id in frame index.]
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:rtype: [bool]
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"""
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data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
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return data
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def isObjectInFrame(self, iD, index):
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"""
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Check if an object id is in a frame index.
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:param [iD]: [Id of the object.]
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:type [index]: [int]
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:param [index]: [Index of the image.]
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:type [index]: [int]
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...
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:return: [True if object id in frame index.]
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:rtype: [bool]
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"""
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data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
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if data.empty:
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return False
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else:
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return True

‎FastAnalysis/tests/__init__.py‎

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‎FastAnalysis/tests/test_load.py‎

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import pytest
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import pandas
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import load
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def test_load_file():
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"""Test that file is loaded as a dataframe."""
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tracking = load.Load("tests/tracking.txt").getDataframe()
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reference = pandas.read_csv("tests/tracking.txt", sep='\t')
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pandas.testing.assert_frame_equal(tracking, reference)
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def test_load_file_error():
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"""Test that wrong path lead to Exception."""
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with pytest.raises(Exception):
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tracking = load.Load("tests/tracing.txt").getDataframe()
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assert tracking
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def test_object_number():
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"""Test number of objects."""
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objectNumber = load.Load("tests/tracking.txt").getObjectNumber()
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assert objectNumber == 207
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def test_get_object():
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"""Test get the data for an object"""
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reference = pandas.read_csv("tests/tracking.txt", sep='\t')
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tracking = load.Load("tests/tracking.txt").getObject(0)
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pandas.testing.assert_frame_equal(tracking, reference[reference.id==0])
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tracking = load.Load("tests/tracking.txt").getObject(1)
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pandas.testing.assert_frame_equal(tracking, reference[reference.id==1])
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def test_get_frame():
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"""Test get the data for a frame"""
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reference = pandas.read_csv("tests/tracking.txt", sep='\t')
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tracking = load.Load("tests/tracking.txt").getFrame(10)
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pandas.testing.assert_frame_equal(tracking, reference[reference.imageNumber==10])
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tracking = load.Load("tests/tracking.txt").getFrame(1)
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pandas.testing.assert_frame_equal(tracking, reference[reference.imageNumber==1])
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def test_get_object_in_frame():
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"""Test get the data for an frame"""
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reference = pandas.read_csv("tests/tracking.txt", sep='\t')
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tracking = load.Load("tests/tracking.txt").getObjectInFrame(0, 200)
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pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==200)&(reference.id==0)])
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tracking = load.Load("tests/tracking.txt").getObjectInFrame(1, 100)
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pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==100)&(reference.id==1)])
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def test_is_object_in_frame():
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"""Test get the data for an frame"""
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reference = pandas.read_csv("tests/tracking.txt", sep='\t')
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tracking = load.Load("tests/tracking.txt").isObjectInFrame(0, 0)
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assert tracking
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tracking = load.Load("tests/tracking.txt").isObjectInFrame(0, 1500)
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assert not tracking
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