diff --git a/.gitignore b/.gitignore index c82b9448..ec67a4a3 100644 --- a/.gitignore +++ b/.gitignore @@ -63,6 +63,7 @@ instance/ # Sphinx documentation docs/_build/ +docs/source/*.md # PyBuilder target/ diff --git a/.travis.yml b/.travis.yml index 61d642e6..348862ad 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,8 +2,8 @@ language: "python" python: - "3.6" install: - - cat requirements.txt | xargs -n 1 -L 1 pip install --no-cache-dir - - pip install -U . + - pip install cython + - pip install -U .[online,test,doc] script: nosetests notifications: email: false diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..ea97d4c7 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,46 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at contact@zooniverse.org. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version] + +[homepage]: http://contributor-covenant.org +[version]: http://contributor-covenant.org/version/1/4/ diff --git a/Contributing.md b/Contributing.md new file mode 100644 index 00000000..ed337c2f --- /dev/null +++ b/Contributing.md @@ -0,0 +1,101 @@ +# Contributing + +## Code Style +Use [PEP8](https://www.python.org/dev/peps/pep-0008/) syntax. + +--- + +## Building Documentation +Automatic documentation will be created using [sphinx](http://www.sphinx-doc.org/en/stable/) so add doc strings to any files created and functions written. Documentation can be compiled with the `make_docs.sh` bash script. + +--- + +## Writing Extractors +Extractors are used to take classifications coming out of Panoptes and extract the relevant data needed to calculate a aggregated answer for one task on a subject. Ideally this extraction should be as flat as possible (i.e. no deeply nested dictionaries), but sometimes this can not be avoided. + +### 1. Make a new function for the extractor + +1. Create a new file for the function in the `extractors` folder +2. Define a new function `*_extractor` that takes in the raw classification json (as it appears in the classification dump `csv` from Panoptes) and returns a `dict`-like object of the extracted data. +3. Use the `@extractor_wrapper` decorator on the function (can be imported with `from .extractor_wrapper import extractor_wrapper`). +4. Use the `@subtask_wrapper` and `@tool_wrapper` decorators if the function is for a drawing tool (can be imported with `from .extractor_wrapper import subtask_extractor_wrapper`). +5. Write tests for the extractor in the `tests/extractor_tests` folder. The `ExtractorTest` class from the `tests/extractor_tests/base_test_class.py` file should be used to create the test function. This class ensures that both the "offline" and "online" versions of the code are tested and produce the expected results. See the other tests in that folder for examples of how to use the `ExtractorTest` class. + +#### The `@extractor_wrapper` decorator + +This decorator removes the boiler plate code that goes along with making a extractor function that works with both the classification dump `csv` files (offline) and API request from caesar (online). If A `request` is passed into the function it will pull the data out as json and pass it into the extractor, if anything else is passed in the function will be called directly. This decorator also does the following: + - filter the classifications using the `task` and `tools` keywords passed into the extractor + - add the aggregation version number to the final extract + +#### The `@subtask_extractor_wrapper` decorator +This decorator removes the boiler plate code that goes along with extracting subtask data from drawing tasks. This decorator looks for the `details` keyword passed into the extractor function and will apply the specified extractor the the proper subtask data and return the extracts as a list in the same order the subtask presented them. + +Note: It is assumed that the first level of the extracted dictionary refers to the subject's frame index (e.g. `frame0` or `frame1`) even when the subject only has one frame. + +#### The `@tool_wrapper` decorator +This decorator removes the boiler plate code for filtering classifications based on the `tools` keyword. This makes it so each tool for a drawing task can have extractors set up independently. + +### 2. Create the route to the extractor +The routes are automatically constructed using the `extractors` dictionary in the `__init__.py` file: + +1. import the new extractor into the `__init__.py` file with the following format `from .*_extractor import *_extractor` +2. Add the `*_extractor` function to the `extractors` dictionary with a sensible route name as the `key` (typically the `key` should be the same as the extractor name) + +### 3. Allow the offline version of the code automatically detect this extractor type from a workflow object + +1. Update the `workflow_config.py` function with the new task type. The value used for the type should be the same `key` used in the `__init__.py` file +2. Update the `tests/utility_tests/test_workflow_config.py` test with this new task type + +### 4. Add to documentation +The code is auto-documented using [sphinx](http://www.sphinx-doc.org/en/stable/index.html). + +1. Add a doc string to every function written and a "heading" doc string at the top of any new files created (follow the [numpy doc string convention](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)) +2. Add a reference to the new file to `docs/source/extractors.rst` +3. Add to the extractor/reducer lookup table `docs/source/Task_lookup_table.rst` +4. Build the docs with the `make_docs.sh` bash script + +### 5. Make sure everything still works +1. run `nosetests` and ensure all tests still pass + +--- + +## Writing Reducers +Reducers are functions that take a list of extracts and combines them into aggregated values. Ideally this reduction should be as flat as possible (i.e. no deeply nested dictionaries), but sometimes this can not be avoided. + +### 1. Make new functions for the reducer +Typically two function need to be defined for a reducer. + +1. `process_data` is a helper function that takes a list of raw extracted data objects and pre-processes them into a form the main reducer function can use (e.g. arranging the data into arrays, creating `Counter` objects, etc...) +2. The `*_reducer` function that takes in the output of the `process_data` function and returns the reduced data as a `dict`-like object. +3. The `*_reducer` function should use the `@reducer_wrapper` decorator with the `process_data` function passed as the `process_data` keyword. +4. If the reducer exposes keywords the user can specify a `DEFAULTS` dictionary must be specified of the form: `DEFAULTS = {'': {'default': , 'type': }}` +5. If these keywords are passed into the `process_data` function they `DEFAULTS` dictionary should be passed into the `@reducer_wrapper` as the `defaults_process` keyword. If these keywords are passed into the main `*_reducer` function the `DEFAULTS` dictionary should be passed into the `@reducer_wrapper` as the `defaults_data` keyword. Note: any combination of these two can be used. +6. Write tests for all the above functions and place them in the `test/reducer_test/` folder. The decorator exposes the original function on the `._original` method of the decorated function, this allows for it to be tested directly. The `ReducerTest` class from the `tests/reducer_tests/base_test_class.py` file should be used to create the test function. This class ensures that both the "offline" and "online" versions of the code are tested and produce the expected results. See the other tests in that folder for examples of how to use the `ReducerTest` class. + +#### The `@reducer_wrapper` decorator + +This decorator removes the boiler plate needed to set up a reducer function to work with extractions from either a `csv` file (offline) or an API request from caesar. It will also run an optional `process_data` data function and pass the results into the wrapped function. Various user defined keywords are also passed into either the `process_data` function or the wrapped function. All keywords are parsed and type-checked before being used, that way no invalid keywords will be passed into either function. This wrapper will also do the following: + - Remove the `aggregation_version` keyword from each extract so it is not passed into the reducer function + - Add the `aggregation_version` keyword to the final reduction dictionary + +#### The `@subtask_reducer_wrapper` decorator +This decorator removes the boiler plate code that goes along with reducing subtask data from drawing tasks. This decorator looks for the `details` keyword passed into the reducer function and will apply the specified reducer the the proper subtask data within each *cluster* found on the subject and returns the reductions as a list in the same order the subtask presented them. + +Note: It is assumed that the first level of the reduced dictionary refers to the subject's frame index (e.g. `frame0` or `frame1`) even when the subject only has one frame. + +### 2. Create the route to the reducer +The routes are automatically constructed using the `reducers` dictionary in the `__init__.py` file: + +1. import the new reducer into the `__init__.py` file with the following format `from .*_reducer import *_reducer` +2. Add the `*_reducer` function to the `reducer` dictionary with a sensible route name as the `key` (typically the `key` should be the same as the reducer name) + +### 3. Add to documentation +The code is auto-documented using [sphinx](http://www.sphinx-doc.org/en/stable/index.html). + +1. Add a doc string to every function written and a "heading" doc string at the top of any new files created (follow the [numpy doc string convention](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)) +2. Add a reference to the new file to `docs/source/reducers.rst` +3. Add to the extractor/reducer lookup table `docs/source/Task_lookup_table.rst` +4. Build the docs with the `make_docs.sh` bash script + +### 4. Make sure everything still works +1. run `nosetests` and ensure all tests still pass diff --git a/Dockerfile b/Dockerfile index 90066695..10edb6d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,12 +4,18 @@ ENV LANG=C.UTF-8 WORKDIR /usr/src/aggregation -# install requirements -COPY requirements.txt ./ RUN pip install --upgrade pip -RUN cat requirements.txt | xargs -n 1 -L 1 pip install --no-cache-dir -COPY . ./ +# this line is still needed until hdbscan pushes to pip next +RUN pip install cython numpy + +# install dependencies +COPY setup.py . +RUN pip install .[online,test,doc] + +# install package +COPY . . +RUN pip install -U .[online,test,doc] # make documentation RUN /bin/bash -lc ./make_docs.sh diff --git a/Dockerfile.bin_cmds b/Dockerfile.bin_cmds index 17ffae14..7dfbb559 100644 --- a/Dockerfile.bin_cmds +++ b/Dockerfile.bin_cmds @@ -4,15 +4,15 @@ ENV LANG=C.UTF-8 WORKDIR /usr/src/aggregation -# install requirements -COPY requirements.txt ./ RUN pip install --upgrade pip -RUN cat requirements.txt | xargs -n 1 -L 1 pip install --no-cache-dir -COPY . ./ -RUN pip install . +# this line is still needed until hdbscan pushes to pip next +RUN pip install cython numpy -# make documentation -RUN /bin/bash -lc ./make_docs.sh +# install dependencies +COPY setup.py . +RUN pip install .[test] -CMD python routes.py +# install package +COPY . . +RUN pip install -U .[test] diff --git a/README.md b/README.md index 1d9fa9c9..f922b352 100644 --- a/README.md +++ b/README.md @@ -1,158 +1,71 @@ -# python-reducers-for-caesar +# Getting started This is a collection of external reducers written for [caesar](https://github.com/zooniverse/caesar) and offline use. -# Documentation -https://aggregation-caesar.zooniverse.org/docs +--- -# Offline use -### With your own python install -To install (python 3 only): +## Documentation +You can find the [latest documentation](https://aggregation-caesar.zooniverse.org/docs) on the aggregations code's website. + +--- + +## Installing for offline use +### With your own python install (python 3 only) +Instal the latest stable release: +```bash +pip install panoptes_aggregation +``` + +Or for development or testing, you can install the development version directly from GitHub: +```bash +pip install -U git+git://github.com/zooniverse/aggregation-for-caesar.git +``` + +Upgrade and existing installation: ```bash -git clone https://github.com/zooniverse/aggregation-for-caesar.git -cd aggregation-for-caesar -pip install . +pip install -U panoptes_aggregation ``` +If you see an error about `Cython` not being installed run `pip install cython` and try `pip install .` again. + ### With Docker -https://docs.docker.com/get-started/ +[https://docs.docker.com/get-started/](https://docs.docker.com/get-started/) -**Using docker-compose** https://docs.docker.com/compose/ +**Using docker-compose** [https://docs.docker.com/compose/](https://docs.docker.com/compose/) ``` docker-compose -f docker-compose.local_scripts.yml build local_scripts ``` -From the root directory of this repository, run the desired python scripts using the docker image, e.g. `extract_panoptes_csv.py --help` +From the root directory of this repository, run the desired python scripts using the docker image, e.g. `config_workflow_panoptes --help` ``` -docker-compose -f docker-compose.local_scripts.yml run --rm local_scripts python bin/extract_panoptes_csv.py --help +docker-compose -f docker-compose.local_scripts.yml run --rm local_scripts config_workflow_panoptes --help ``` **Or directly via docker** ``` docker build . -f Dockerfile.bin_cmds -t aggregation_for_caesar ``` -From the root directory of this repository, run the desired python scripts using the docker image, e.g. `extract_panoptes_csv.py --help` +From the root directory of this repository, run the desired python scripts using the docker image, e.g. `config_workflow_panoptes --help` ``` -docker run -it --rm --name extract_panoptes_csv -v "$PWD":/usr/src/aggregation aggregation_for_caesar python bin/extract_panoptes_csv.py --help +docker run -it --rm --name config_workflow_panoptes -v "$PWD":/usr/src/aggregation aggregation_for_caesar config_workflow_panoptes --help ``` -## Download your data from the project builder -You will need two files for offline use: - - The classification dump: The `Request new classification export` or `Request new workflow classification export` button from the lab's `Data Export` tab - - The workflow dump: The `Request new workflow export` button from the lab's `Data Export` tab - -## Extracting data -Note: this only works for question tasks and the drawing tool's point data at the moment +--- -Use the command line tool to extract your data into one flat `csv` file for each extractor used: +## Installing for online use +The docker file included is ready to be deployed on any server. Once deployed, the extractors will be available on the `/extractors/` routes and the reducers will be available on the `/reducers/` routes. Any keywords passed into these functions should be included as url parameters on the route (e.g. `https://aggregation-caesar.zooniverse.org/extractors/point_extractor_by_frame?task=T0`). For more complex keywords (e.g. `detals` for subtasks), python's [urllib.parse.urlencode](https://docs.python.org/3/library/urllib.parse.html#urllib.parse.urlencode) can be used to translate a keyword list into the proper url encoding. -```bash -usage: extract_panoptes_csv.py [-h] [-v VERSION] [-k KEYWORDS] [-H] [-O] - [-o OUTPUT] - classification_csv workflow_csv workflow_id - -extract data from panoptes classifications based on the workflow - -positional arguments: - classification_csv the classificaiton csv file containing the panoptes - data dump - workflow_csv the csv file containing the workflow data - workflow_id the workflow ID you would like to extract - -optional arguments: - -h, --help show this help message and exit - -v VERSION, --version VERSION - the workflow version to extract - -k KEYWORDS, --keywords KEYWORDS - keywords to be passed into the extractor for a task in - the form of a json string, e.g. '{"T0": {"dot_freq": - "line"} }' (note: double quotes must be used inside - the brackets) - -H, --human switch to make the data column labels use the task and - question labels instead of generic labels - -O, --order arrange the data columns in alphabetical order before - saving - -o OUTPUT, --output OUTPUT - the base name for output csv file to store the - annotation extractions (one file will be created for - each extractor used) -``` - -example usage: -```bash -extract_panoptes_csv.py mark-galaxy-centers-and-foreground-stars-classifications.csv galaxy-zoo-3d-workflows.csv 3513 -v 1 -o galaxy_center_and_star_mpl5.csv -``` -This will extract the user drawn data points from workflow `3513` with a major version of `1` and place them in a `csv` file named `point_extractor_galaxy_center_and_star_mpl5.csv`. +The documentation will be built and available on the `/docs` route. -## Reducing data -Note: this only works for question tasks and the drawing tool's point data at the moment - -```bash -usage: reduce_panoptes_csv.py [-h] [-F {first,last,all}] [-k KEYWORDS] - [-o OUTPUT] - extracted_csv - -reduce data from panoptes classifications based on the extracted data (see -extract_panoptes_csv) - -positional arguments: - extracted_csv the extracted csv file output from - extract_panoptes_csv - -optional arguments: - -h, --help show this help message and exit - -F {first,last,all}, --filter {first,last,all} - how to filter a user makeing multiple classifications - for one subject - -k KEYWORDS, --keywords KEYWORDS - keywords to be passed into the reducer in the form of - a json string, e.g. '{"eps": 5.5, "min_samples": 3}' - (note: double quotes must be used inside the brackets) - -o OUTPUT, --output OUTPUT - the base name for output csv file to store the - reductions - -s, --stream stream output to csv after each redcution (this is - slower but is resumable) -``` - -example usage: -```bash -reduce_panoptes_csv.py point_extractor_galaxy_center_and_star_mpl5.csv -F first -k '{"eps": 5, "min_sample": 3}' -o 'galaxy_and_star_mpl5.csv' -``` -This will produce a reduced `csv` file named `point_reducer_galaxy_and_star_mpl5.csv`. If a user classified an image more than once only the first one is kept. - -## reading csv files in python -The resulting csv files typically contain arrays as values. These arrays are typically read in as strings by most csv readers. To make it easier to read these files in a "science ready" way a utility function for `pandas.read_csv` is provided in `panoptes_aggregation.csv_utils`: -```python -import pandas -from panoptes_aggregation.csv_utils import unjson_dataframe - -# the `data.*` columns are read in as strings instead of arrays -data = pandas.read_csv('point_reducer_galaxy_and_star_mpl5.csv') - -# use unjson_dataframe to convert them to lists -# all values are updated in place leaving null values untouched -unjson_dataframe(data) -``` - -# Caesar - -## Build/run the app in docker +### Build/run the app in docker locally To run a local version use: ```bash docker-compose build docker-compose up ``` -and listen on `localhost:5000`. The documentation will automatically be created and added to the '/docs' route. +and listen on `localhost:5000`. -## run tests +### Running tests in the docker container To run the tests use: ```bash -docker-compose run aggregation /bin/bash -lc "nosetests" +docker-compose run --rm aggregation nosetests ``` - -# Contributing - -1. Use [PEP8](https://www.python.org/dev/peps/pep-0008/) syntax -2. Automatic documentation will be created using [sphinx](http://www.sphinx-doc.org/en/stable/) so add doc strings to any files created and functions written -3. A guide for writing [extractors](panoptes_aggregation/extractors/README.md) -4. A guide for writing [reducers](panoptes_aggregation/reducers/README.md) diff --git a/Scripts.md b/Scripts.md new file mode 100644 index 00000000..2c1fe9f7 --- /dev/null +++ b/Scripts.md @@ -0,0 +1,210 @@ +# Using the command line scripts +This package comes with several command line scripts for use with the `csv` data dumps produced by Panoptes. + +## Download your data from the project builder +You will need two to three files from your project for offline use: + - The classification dump: The `Request new classification export` or `Request new workflow classification export` button from the lab's `Data Export` tab + - The workflow dump: The `Request new workflow export` button from the lab's `Data Export` tab + - The workflow contents (optional): The `Request new workflow contents export` button from the lab's `Data Export` tab. This file is used to make a look up table between the column names used for each task/answer/tool and the original text used for them on the project. + +### Example: Penguin Watch +Penguin Watch has several workflows, for this example we will look at workflow number 6465 (time lapse cameras) and version `57.76`. The downloaded files for this project are: + - `penguin-watch-workflows.csv`: the workflow file (contains the major version number as a column) + - `penguin-watch-workflow_contents.csv`: the workflow contents file (contains the minor version number as a column) + - `time-lapse-cameras-classifications.csv`: the classification file for workflow 6465 + +--- + +## Configure the extractors and reducers +Use the command line tool to make configuration `yaml` files that are used to set up the extractors and reducers. These base files will use the default settings for various task types. They can be adjusted if the defaults are not needed (e.g. you don't need to extract all the tasks, or you need more control over the reducer's settings). + +```bash +usage: config_workflow_panoptes [-h] [-v VERSION] [-k KEYWORDS] + [-c WORKFLOW_CONTENT] [-m MINOR_VERSION] + workflow_csv workflow_id + +Make configuration files for panoptes data extraction and reduction based on a +workflow export + +positional arguments: + workflow_csv the csv file containing the workflow data + workflow_id the workflow ID you would like to extract + +optional arguments: + -h, --help show this help message and exit + -v VERSION, --version VERSION + The major workflow version to extract + -k KEYWORDS, --keywords KEYWORDS + keywords to be passed into the configuration of a task + in the form of a json string, e.g. '{"T0": + {"dot_freq": "line"} }' (note: double quotes must be + used inside the brackets) + -c WORKFLOW_CONTENT, --workflow_content WORKFLOW_CONTENT + The (optional) workflow content file can be provided + to create a lookup table for task/answer/tool numbers + to the text used on the workflow. + -m MINOR_VERSION, --minor_version MINOR_VERSION + The minor workflow version used to create the lookup + table for the workflow content + -l LANGUAGE, --language LANGUAGE + The language to use for the workflow content +``` + +### Example: Penguin Watch +```bash +config_workflow_panoptes penguin-watch-workflows.csv 6465 -v 52 -c penguin-watch-workflow_contents.csv -m 76 +``` + +This creates four files: + - `Extractor_config_workflow_6465_V52.yaml`: The configuration for the extractor code + - `Reducer_config_workflow_6465_V52_point_extractor_by_frame.yaml`: The configuration for the reducer used for the point task + - `Reducer_config_workflow_6465_V52_question_extractor.yaml`: The configuration for the reducer used for the question task + - `Task_labels_workflow_6465_V52.76.yaml`: A lookup table to translate the column names used in the extractor/reducer output files into the text originally used on the workflow. + +--- + +## Extracting data +Note: this only works for some task types, see the [documentation](https://aggregation-caesar.zooniverse.org/docs) for a full list of supported task types. + +Use the command line tool to extract your data into one flat `csv` file for each task type: + +```bash +usage: extract_panoptes_csv [-h] [-O] [-o OUTPUT] + classification_csv extractor_config + +extract data from panoptes classifications based on the workflow + +positional arguments: + classification_csv the classification csv file containing the panoptes + data dump + extractor_config the extractor configuration yaml file produced by + `config_workflow_panoptes` + +optional arguments: + -h, --help show this help message and exit + -O, --order arrange the data columns in alphabetical order before + saving + -o OUTPUT, --output OUTPUT + the base name for output csv file to store the + annotation extractions (one file will be created for + each extractor used) +``` + +### Example: Penguin Watch +Before starting let's take a closer look at the extractor configuration file `Extractor_config_workflow_6465_V52.yaml`: +```yaml +extractor_config: + point_extractor_by_frame: + - details: + T0_tool3: + - question_extractor + task: T0 + tools: + - 0 + - 1 + - 2 + - 3 + question_extractor: + - task: T1 +workflow_id: 6465 +workflow_version: 52 +``` +This shows the basic setup for what extractor will be used for each task. From this configuration we can see that the point extractor will be used for each of the tools in task `T0`, `tool3` of that task will have the question extractor run on its sub-task, and a question extractor will be used for tasks `T1`. If any of these extractions are not desired they can be deleted from this file before running the extractor. In this case task `T4` was on the original workflow but was never used on the final project, I have already removed it from the configuration above. + +Note: If a workflow contains any task types that don't have extractors or reducers they will not show up in this config file. + +```bash +extract_panoptes_csv time-lapse-cameras-classifications.csv Extractor_config_workflow_6465_V52.yaml -o example +``` + +This creates two `csv` files (one for each extractor listed in the config file): + - `question_extractor_example.csv` + - `point_extractor_by_frame_example.csv` + +--- + +## Reducing data +Note: this only works for some task types, see the [documentation](https://aggregation-caesar.zooniverse.org/docs) for a full list of supported task types. + +```bash +usage: reduce_panoptes_csv [-h] [-F {first,last,all}] [-O] [-o OUTPUT] [-s] + extracted_csv reducer_config + +reduce data from panoptes classifications based on the extracted data (see +extract_panoptes_csv) + +positional arguments: + extracted_csv the extracted csv file output from + extract_panoptes_csv + reducer_config the reducer yaml file output from + config_workflow_panoptes + +optional arguments: + -h, --help show this help message and exit + -F {first,last,all}, --filter {first,last,all} + how to filter a user making multiple classifications + for one subject + -O, --order arrange the data columns in alphabetical order before + saving + -o OUTPUT, --output OUTPUT + the base name for output csv file to store the + reductions + -s, --stream stream output to csv after each reduction (this is + slower but is resumable) +``` + +### Example: Penguin Watch +For this example we will do the point clustering for the task `T0`. Let's take a look at the default config file for that reducer `Reducer_config_workflow_6465_V52_point_extractor_by_frame.yaml`: +```yaml +reducer_config: + point_reducer_dbscan: + details: + T0_tool3: + - question_reducer +``` + +As we can see, the default reducer is `point_reducer_dbscan` and the only keyword specified is the only associated with the sub-task of `tool3`. To get better results we will add some clustering keywords to the configuration of `DBSCAN`: +```yaml +reducer_config: + point_reducer_dbscan: + eps: 5 + min_samples: 3 + details: + T0_tool3: + - question_reducer +``` + +But for this project there is a large amount of depth-of-field in the images, leading to a non-constant density of point clusters across the images (more dense in the background of the image and less dense in the foreground). This means that `HDBSCAN` will work better: +```yaml +reducer_config: + point_reducer_hdbscan: + min_cluster_size: 4 + min_samples: 3 + details: + T0_tool3: + - question_reducer +``` + +Now that it is set up we can run: +```bash +reduce_panoptes_csv point_extractor_by_frame_example.csv Reducer_config_workflow_6465_V52_point_extractor_by_frame.yaml -o example +``` + +This will create one file: + - `point_reducer_hdbscan_example.csv`: The clustered data points for task `T0` + +--- + +## Reading csv files in python +The resulting csv files typically contain arrays as values. These arrays are read in as strings by most csv readers. To make it easier to read these files in a "science ready" way a utility function for `pandas.read_csv` is provided in `panoptes_aggregation.csv_utils`: +```python +import pandas +from panoptes_aggregation.csv_utils import unjson_dataframe + +# the `data.*` columns are read in as strings instead of arrays +data = pandas.read_csv('point_reducer_hdbscan_example.csv') + +# use unjson_dataframe to convert them to lists +# all values are updated in place leaving null values untouched +unjson_dataframe(data) +``` diff --git a/docs/.buildinfo b/docs/.buildinfo deleted file mode 100644 index 26ec882d..00000000 --- a/docs/.buildinfo +++ /dev/null @@ -1,4 +0,0 @@ -# Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: abad03352894d9f4a23fc827060722b2 -tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_sources/extractros.rst.txt b/docs/_sources/extractros.rst.txt deleted file mode 100644 index 38d01f32..00000000 --- a/docs/_sources/extractros.rst.txt +++ /dev/null @@ -1,32 +0,0 @@ -Extractors -========== - -.. automodule:: panoptes_aggregation.extractors.question_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.point_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.rectangle_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.survey_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.poly_line_text_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.line_text_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.sw_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.sw_variant_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.sw_graphic_extractor - :members: - -.. automodule:: panoptes_aggregation.extractors.dropdown_extractor - :members: diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt deleted file mode 100644 index ea0efd96..00000000 --- a/docs/_sources/index.rst.txt +++ /dev/null @@ -1,21 +0,0 @@ -.. panoptes_aggregation documentation master file, created by - sphinx-quickstart on Mon Aug 7 13:22:24 2017. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to panoptes_aggregation's documentation! -================================================ - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - extractros - reducers - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/_sources/reducers.rst.txt b/docs/_sources/reducers.rst.txt deleted file mode 100644 index c62048a0..00000000 --- a/docs/_sources/reducers.rst.txt +++ /dev/null @@ -1,29 +0,0 @@ -Reducers -======== - -.. automodule:: panoptes_aggregation.reducers.question_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.point_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.point_reducer_hdbscan - :members: - -.. automodule:: panoptes_aggregation.reducers.rectangle_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.survey_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.poly_line_text_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.text_utils - :members: - -.. automodule:: panoptes_aggregation.reducers.sw_variant_reducer - :members: - -.. automodule:: panoptes_aggregation.reducers.dropdown_reducer - :members: diff --git a/docs/_static/ajax-loader.gif b/docs/_static/ajax-loader.gif deleted file mode 100644 index 61faf8ca..00000000 Binary files a/docs/_static/ajax-loader.gif and /dev/null differ diff --git a/docs/_static/basic.css b/docs/_static/basic.css deleted file mode 100644 index 6df76b0a..00000000 --- a/docs/_static/basic.css +++ /dev/null @@ -1,639 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; 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' + _('Hide Search Matches') + '

') - .appendTo($('#searchbox')); - } - }, - - /** - * init the domain index toggle buttons - */ - initIndexTable : function() { - var togglers = $('img.toggler').click(function() { - var src = $(this).attr('src'); - var idnum = $(this).attr('id').substr(7); - $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) == 'minus.png') - $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); - else - $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); - }).css('display', ''); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { - togglers.click(); - } - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords : function() { - $('#searchbox .highlight-link').fadeOut(300); - $('span.highlighted').removeClass('highlighted'); - }, - - /** - * make the url absolute - */ - makeURL : function(relativeURL) { - return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; - }, - - /** - * get the current relative url - */ - getCurrentURL : function() { - var path = document.location.pathname; - var parts = path.split(/\//); - $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this == '..') - parts.pop(); - }); - var url = parts.join('/'); - return path.substring(url.lastIndexOf('/') + 1, path.length - 1); - }, - - initOnKeyListeners: function() { - $(document).keyup(function(event) { - var activeElementType = document.activeElement.tagName; - // don't navigate when in search box or textarea - if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { - switch (event.keyCode) { - case 37: // left - var prevHref = $('link[rel="prev"]').prop('href'); - if (prevHref) { - window.location.href = prevHref; - return false; - } - case 39: // right - var nextHref = $('link[rel="next"]').prop('href'); - if (nextHref) { - window.location.href = nextHref; - return false; - } - } - } - }); - } -}; - -// quick alias for translations -_ = Documentation.gettext; - -$(document).ready(function() { - Documentation.init(); -}); \ No newline at end of file diff --git a/docs/_static/down-pressed.png b/docs/_static/down-pressed.png deleted file mode 100644 index 5756c8ca..00000000 Binary files a/docs/_static/down-pressed.png and /dev/null differ diff --git a/docs/_static/down.png b/docs/_static/down.png deleted file mode 100644 index 1b3bdad2..00000000 Binary files a/docs/_static/down.png and /dev/null differ diff --git a/docs/_static/file.png b/docs/_static/file.png deleted file mode 100644 index a858a410..00000000 Binary files a/docs/_static/file.png and /dev/null differ diff --git a/docs/_static/jquery-3.1.0.js b/docs/_static/jquery-3.1.0.js deleted file mode 100644 index f2fc2747..00000000 --- a/docs/_static/jquery-3.1.0.js +++ /dev/null @@ -1,10074 +0,0 @@ -/*eslint-disable no-unused-vars*/ -/*! - * jQuery JavaScript Library v3.1.0 - * https://jquery.com/ - * - * Includes Sizzle.js - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * https://jquery.org/license - * - * Date: 2016-07-07T21:44Z - */ -( function( global, factory ) { - - "use strict"; - - if ( typeof module === "object" && typeof module.exports === "object" ) { - - // For CommonJS and CommonJS-like environments where a proper `window` - // is present, execute the factory and get jQuery. - // For environments that do not have a `window` with a `document` - // (such as Node.js), expose a factory as module.exports. - // This accentuates the need for the creation of a real `window`. - // e.g. var jQuery = require("jquery")(window); - // See ticket #14549 for more info. - module.exports = global.document ? - factory( global, true ) : - function( w ) { - if ( !w.document ) { - throw new Error( "jQuery requires a window with a document" ); - } - return factory( w ); - }; - } else { - factory( global ); - } - -// Pass this if window is not defined yet -} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { - -// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 -// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode -// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common -// enough that all such attempts are guarded in a try block. -"use strict"; - -var arr = []; - -var document = window.document; - -var getProto = Object.getPrototypeOf; - -var slice = arr.slice; - -var concat = arr.concat; - -var push = arr.push; - -var indexOf = arr.indexOf; - -var class2type = {}; - -var toString = class2type.toString; - -var hasOwn = class2type.hasOwnProperty; - -var fnToString = hasOwn.toString; - -var ObjectFunctionString = fnToString.call( Object ); - -var support = {}; - - - - function DOMEval( code, doc ) { - doc = doc || document; - - var script = doc.createElement( "script" ); - - script.text = code; - doc.head.appendChild( script ).parentNode.removeChild( script ); - } -/* global Symbol */ -// Defining this global in .eslintrc would create a danger of using the global -// unguarded in another place, it seems safer to define global only for this module - - - -var - version = "3.1.0", - - // Define a local copy of jQuery - jQuery = function( selector, context ) { - - // The jQuery object is actually just the init constructor 'enhanced' - // Need init if jQuery is called (just allow error to be thrown if not included) - return new jQuery.fn.init( selector, context ); - }, - - // Support: Android <=4.0 only - // Make sure we trim BOM and NBSP - rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, - - // Matches dashed string for camelizing - rmsPrefix = /^-ms-/, - rdashAlpha = /-([a-z])/g, - - // Used by jQuery.camelCase as callback to replace() - fcamelCase = function( all, letter ) { - return letter.toUpperCase(); - }; - -jQuery.fn = jQuery.prototype = { - - // The current version of jQuery being used - jquery: version, - - constructor: jQuery, - - // The default length of a jQuery object is 0 - length: 0, - - toArray: function() { - return slice.call( this ); - }, - - // Get the Nth element in the matched element set OR - // Get the whole matched element set as a clean array - get: function( num ) { - return num != null ? - - // Return just the one element from the set - ( num < 0 ? this[ num + this.length ] : this[ num ] ) : - - // Return all the elements in a clean array - slice.call( this ); - }, - - // Take an array of elements and push it onto the stack - // (returning the new matched element set) - pushStack: function( elems ) { - - // Build a new jQuery matched element set - var ret = jQuery.merge( this.constructor(), elems ); - - // Add the old object onto the stack (as a reference) - ret.prevObject = this; - - // Return the newly-formed element set - return ret; - }, - - // Execute a callback for every element in the matched set. - each: function( callback ) { - return jQuery.each( this, callback ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map( this, function( elem, i ) { - return callback.call( elem, i, elem ); - } ) ); - }, - - slice: function() { - return this.pushStack( slice.apply( this, arguments ) ); - }, - - first: function() { - return this.eq( 0 ); - }, - - last: function() { - return this.eq( -1 ); - }, - - eq: function( i ) { - var len = this.length, - j = +i + ( i < 0 ? len : 0 ); - return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); - }, - - end: function() { - return this.prevObject || this.constructor(); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: arr.sort, - splice: arr.splice -}; - -jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, - target = arguments[ 0 ] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - - // Skip the boolean and the target - target = arguments[ i ] || {}; - i++; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction( target ) ) { - target = {}; - } - - // Extend jQuery itself if only one argument is passed - if ( i === length ) { - target = this; - i--; - } - - for ( ; i < length; i++ ) { - - // Only deal with non-null/undefined values - if ( ( options = arguments[ i ] ) != null ) { - - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject( copy ) || - ( copyIsArray = jQuery.isArray( copy ) ) ) ) { - - if ( copyIsArray ) { - copyIsArray = false; - clone = src && jQuery.isArray( src ) ? src : []; - - } else { - clone = src && jQuery.isPlainObject( src ) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend( { - - // Unique for each copy of jQuery on the page - expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), - - // Assume jQuery is ready without the ready module - isReady: true, - - error: function( msg ) { - throw new Error( msg ); - }, - - noop: function() {}, - - isFunction: function( obj ) { - return jQuery.type( obj ) === "function"; - }, - - isArray: Array.isArray, - - isWindow: function( obj ) { - return obj != null && obj === obj.window; - }, - - isNumeric: function( obj ) { - - // As of jQuery 3.0, isNumeric is limited to - // strings and numbers (primitives or objects) - // that can be coerced to finite numbers (gh-2662) - var type = jQuery.type( obj ); - return ( type === "number" || type === "string" ) && - - // parseFloat NaNs numeric-cast false positives ("") - // ...but misinterprets leading-number strings, particularly hex literals ("0x...") - // subtraction forces infinities to NaN - !isNaN( obj - parseFloat( obj ) ); - }, - - isPlainObject: function( obj ) { - var proto, Ctor; - - // Detect obvious negatives - // Use toString instead of jQuery.type to catch host objects - if ( !obj || toString.call( obj ) !== "[object Object]" ) { - return false; - } - - proto = getProto( obj ); - - // Objects with no prototype (e.g., `Object.create( null )`) are plain - if ( !proto ) { - return true; - } - - // Objects with prototype are plain iff they were constructed by a global Object function - Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; - return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; - }, - - isEmptyObject: function( obj ) { - - /* eslint-disable no-unused-vars */ - // See https://github.com/eslint/eslint/issues/6125 - var name; - - for ( name in obj ) { - return false; - } - return true; - }, - - type: function( obj ) { - if ( obj == null ) { - return obj + ""; - } - - // Support: Android <=2.3 only (functionish RegExp) - return typeof obj === "object" || typeof obj === "function" ? - class2type[ toString.call( obj ) ] || "object" : - typeof obj; - }, - - // Evaluates a script in a global context - globalEval: function( code ) { - DOMEval( code ); - }, - - // Convert dashed to camelCase; used by the css and data modules - // Support: IE <=9 - 11, Edge 12 - 13 - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); - }, - - each: function( obj, callback ) { - var length, i = 0; - - if ( isArrayLike( obj ) ) { - length = obj.length; - for ( ; i < length; i++ ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } else { - for ( i in obj ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } - - return obj; - }, - - // Support: Android <=4.0 only - trim: function( text ) { - return text == null ? - "" : - ( text + "" ).replace( rtrim, "" ); - }, - - // results is for internal usage only - makeArray: function( arr, results ) { - var ret = results || []; - - if ( arr != null ) { - if ( isArrayLike( Object( arr ) ) ) { - jQuery.merge( ret, - typeof arr === "string" ? - [ arr ] : arr - ); - } else { - push.call( ret, arr ); - } - } - - return ret; - }, - - inArray: function( elem, arr, i ) { - return arr == null ? -1 : indexOf.call( arr, elem, i ); - }, - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - merge: function( first, second ) { - var len = +second.length, - j = 0, - i = first.length; - - for ( ; j < len; j++ ) { - first[ i++ ] = second[ j ]; - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, invert ) { - var callbackInverse, - matches = [], - i = 0, - length = elems.length, - callbackExpect = !invert; - - // Go through the array, only saving the items - // that pass the validator function - for ( ; i < length; i++ ) { - callbackInverse = !callback( elems[ i ], i ); - if ( callbackInverse !== callbackExpect ) { - matches.push( elems[ i ] ); - } - } - - return matches; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var length, value, - i = 0, - ret = []; - - // Go through the array, translating each of the items to their new values - if ( isArrayLike( elems ) ) { - length = elems.length; - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - - // Go through every key on the object, - } else { - for ( i in elems ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - } - - // Flatten any nested arrays - return concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - var tmp, args, proxy; - - if ( typeof context === "string" ) { - tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - args = slice.call( arguments, 2 ); - proxy = function() { - return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || jQuery.guid++; - - return proxy; - }, - - now: Date.now, - - // jQuery.support is not used in Core but other projects attach their - // properties to it so it needs to exist. - support: support -} ); - -if ( typeof Symbol === "function" ) { - jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; -} - -// Populate the class2type map -jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), -function( i, name ) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -} ); - -function isArrayLike( obj ) { - - // Support: real iOS 8.2 only (not reproducible in simulator) - // `in` check used to prevent JIT error (gh-2145) - // hasOwn isn't used here due to false negatives - // regarding Nodelist length in IE - var length = !!obj && "length" in obj && obj.length, - type = jQuery.type( obj ); - - if ( type === "function" || jQuery.isWindow( obj ) ) { - return false; - } - - return type === "array" || length === 0 || - typeof length === "number" && length > 0 && ( length - 1 ) in obj; -} -var Sizzle = -/*! - * Sizzle CSS Selector Engine v2.3.0 - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2016-01-04 - */ -(function( window ) { - -var i, - support, - Expr, - getText, - isXML, - tokenize, - compile, - select, - outermostContext, - sortInput, - hasDuplicate, - - // Local document vars - setDocument, - document, - docElem, - documentIsHTML, - rbuggyQSA, - rbuggyMatches, - matches, - contains, - - // Instance-specific data - expando = "sizzle" + 1 * new Date(), - preferredDoc = window.document, - dirruns = 0, - done = 0, - classCache = createCache(), - tokenCache = createCache(), - compilerCache = createCache(), - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - } - return 0; - }, - - // Instance methods - hasOwn = ({}).hasOwnProperty, - arr = [], - pop = arr.pop, - push_native = arr.push, - push = arr.push, - slice = arr.slice, - // Use a stripped-down indexOf as it's faster than native - // https://jsperf.com/thor-indexof-vs-for/5 - indexOf = function( list, elem ) { - var i = 0, - len = list.length; - for ( ; i < len; i++ ) { - if ( list[i] === elem ) { - return i; - } - } - return -1; - }, - - booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", - - // Regular expressions - - // http://www.w3.org/TR/css3-selectors/#whitespace - whitespace = "[\\x20\\t\\r\\n\\f]", - - // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier - identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", - - // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors - attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + - // Operator (capture 2) - "*([*^$|!~]?=)" + whitespace + - // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" - "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + - "*\\]", - - pseudos = ":(" + identifier + ")(?:\\((" + - // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: - // 1. quoted (capture 3; capture 4 or capture 5) - "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + - // 2. simple (capture 6) - "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + - // 3. anything else (capture 2) - ".*" + - ")\\)|)", - - // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter - rwhitespace = new RegExp( whitespace + "+", "g" ), - rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), - - rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), - rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), - - rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), - - rpseudo = new RegExp( pseudos ), - ridentifier = new RegExp( "^" + identifier + "$" ), - - matchExpr = { - "ID": new RegExp( "^#(" + identifier + ")" ), - "CLASS": new RegExp( "^\\.(" + identifier + ")" ), - "TAG": new RegExp( "^(" + identifier + "|[*])" ), - "ATTR": new RegExp( "^" + attributes ), - "PSEUDO": new RegExp( "^" + pseudos ), - "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + - "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + - "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), - "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), - // For use in libraries implementing .is() - // We use this for POS matching in `select` - "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + - whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) - }, - - rinputs = /^(?:input|select|textarea|button)$/i, - rheader = /^h\d$/i, - - rnative = /^[^{]+\{\s*\[native \w/, - - // Easily-parseable/retrievable ID or TAG or CLASS selectors - rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, - - rsibling = /[+~]/, - - // CSS escapes - // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters - runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), - funescape = function( _, escaped, escapedWhitespace ) { - var high = "0x" + escaped - 0x10000; - // NaN means non-codepoint - // Support: Firefox<24 - // Workaround erroneous numeric interpretation of +"0x" - return high !== high || escapedWhitespace ? - escaped : - high < 0 ? - // BMP codepoint - String.fromCharCode( high + 0x10000 ) : - // Supplemental Plane codepoint (surrogate pair) - String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); - }, - - // CSS string/identifier serialization - // https://drafts.csswg.org/cssom/#common-serializing-idioms - rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\x80-\uFFFF\w-]/g, - fcssescape = function( ch, asCodePoint ) { - if ( asCodePoint ) { - - // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER - if ( ch === "\0" ) { - return "\uFFFD"; - } - - // Control characters and (dependent upon position) numbers get escaped as code points - return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; - } - - // Other potentially-special ASCII characters get backslash-escaped - return "\\" + ch; - }, - - // Used for iframes - // See setDocument() - // Removing the function wrapper causes a "Permission Denied" - // error in IE - unloadHandler = function() { - setDocument(); - }, - - disabledAncestor = addCombinator( - function( elem ) { - return elem.disabled === true; - }, - { dir: "parentNode", next: "legend" } - ); - -// Optimize for push.apply( _, NodeList ) -try { - push.apply( - (arr = slice.call( preferredDoc.childNodes )), - preferredDoc.childNodes - ); - // Support: Android<4.0 - // Detect silently failing push.apply - arr[ preferredDoc.childNodes.length ].nodeType; -} catch ( e ) { - push = { apply: arr.length ? - - // Leverage slice if possible - function( target, els ) { - push_native.apply( target, slice.call(els) ); - } : - - // Support: IE<9 - // Otherwise append directly - function( target, els ) { - var j = target.length, - i = 0; - // Can't trust NodeList.length - while ( (target[j++] = els[i++]) ) {} - target.length = j - 1; - } - }; -} - -function Sizzle( selector, context, results, seed ) { - var m, i, elem, nid, match, groups, newSelector, - newContext = context && context.ownerDocument, - - // nodeType defaults to 9, since context defaults to document - nodeType = context ? context.nodeType : 9; - - results = results || []; - - // Return early from calls with invalid selector or context - if ( typeof selector !== "string" || !selector || - nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { - - return results; - } - - // Try to shortcut find operations (as opposed to filters) in HTML documents - if ( !seed ) { - - if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { - setDocument( context ); - } - context = context || document; - - if ( documentIsHTML ) { - - // If the selector is sufficiently simple, try using a "get*By*" DOM method - // (excepting DocumentFragment context, where the methods don't exist) - if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { - - // ID selector - if ( (m = match[1]) ) { - - // Document context - if ( nodeType === 9 ) { - if ( (elem = context.getElementById( m )) ) { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( elem.id === m ) { - results.push( elem ); - return results; - } - } else { - return results; - } - - // Element context - } else { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( newContext && (elem = newContext.getElementById( m )) && - contains( context, elem ) && - elem.id === m ) { - - results.push( elem ); - return results; - } - } - - // Type selector - } else if ( match[2] ) { - push.apply( results, context.getElementsByTagName( selector ) ); - return results; - - // Class selector - } else if ( (m = match[3]) && support.getElementsByClassName && - context.getElementsByClassName ) { - - push.apply( results, context.getElementsByClassName( m ) ); - return results; - } - } - - // Take advantage of querySelectorAll - if ( support.qsa && - !compilerCache[ selector + " " ] && - (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { - - if ( nodeType !== 1 ) { - newContext = context; - newSelector = selector; - - // qSA looks outside Element context, which is not what we want - // Thanks to Andrew Dupont for this workaround technique - // Support: IE <=8 - // Exclude object elements - } else if ( context.nodeName.toLowerCase() !== "object" ) { - - // Capture the context ID, setting it first if necessary - if ( (nid = context.getAttribute( "id" )) ) { - nid = nid.replace( rcssescape, fcssescape ); - } else { - context.setAttribute( "id", (nid = expando) ); - } - - // Prefix every selector in the list - groups = tokenize( selector ); - i = groups.length; - while ( i-- ) { - groups[i] = "#" + nid + " " + toSelector( groups[i] ); - } - newSelector = groups.join( "," ); - - // Expand context for sibling selectors - newContext = rsibling.test( selector ) && testContext( context.parentNode ) || - context; - } - - if ( newSelector ) { - try { - push.apply( results, - newContext.querySelectorAll( newSelector ) - ); - return results; - } catch ( qsaError ) { - } finally { - if ( nid === expando ) { - context.removeAttribute( "id" ); - } - } - } - } - } - } - - // All others - return select( selector.replace( rtrim, "$1" ), context, results, seed ); -} - -/** - * Create key-value caches of limited size - * @returns {function(string, object)} Returns the Object data after storing it on itself with - * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) - * deleting the oldest entry - */ -function createCache() { - var keys = []; - - function cache( key, value ) { - // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) - if ( keys.push( key + " " ) > Expr.cacheLength ) { - // Only keep the most recent entries - delete cache[ keys.shift() ]; - } - return (cache[ key + " " ] = value); - } - return cache; -} - -/** - * Mark a function for special use by Sizzle - * @param {Function} fn The function to mark - */ -function markFunction( fn ) { - fn[ expando ] = true; - return fn; -} - -/** - * Support testing using an element - * @param {Function} fn Passed the created element and returns a boolean result - */ -function assert( fn ) { - var el = document.createElement("fieldset"); - - try { - return !!fn( el ); - } catch (e) { - return false; - } finally { - // Remove from its parent by default - if ( el.parentNode ) { - el.parentNode.removeChild( el ); - } - // release memory in IE - el = null; - } -} - -/** - * Adds the same handler for all of the specified attrs - * @param {String} attrs Pipe-separated list of attributes - * @param {Function} handler The method that will be applied - */ -function addHandle( attrs, handler ) { - var arr = attrs.split("|"), - i = arr.length; - - while ( i-- ) { - Expr.attrHandle[ arr[i] ] = handler; - } -} - -/** - * Checks document order of two siblings - * @param {Element} a - * @param {Element} b - * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b - */ -function siblingCheck( a, b ) { - var cur = b && a, - diff = cur && a.nodeType === 1 && b.nodeType === 1 && - a.sourceIndex - b.sourceIndex; - - // Use IE sourceIndex if available on both nodes - if ( diff ) { - return diff; - } - - // Check if b follows a - if ( cur ) { - while ( (cur = cur.nextSibling) ) { - if ( cur === b ) { - return -1; - } - } - } - - return a ? 1 : -1; -} - -/** - * Returns a function to use in pseudos for input types - * @param {String} type - */ -function createInputPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for buttons - * @param {String} type - */ -function createButtonPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for :enabled/:disabled - * @param {Boolean} disabled true for :disabled; false for :enabled - */ -function createDisabledPseudo( disabled ) { - // Known :disabled false positives: - // IE: *[disabled]:not(button, input, select, textarea, optgroup, option, menuitem, fieldset) - // not IE: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable - return function( elem ) { - - // Check form elements and option elements for explicit disabling - return "label" in elem && elem.disabled === disabled || - "form" in elem && elem.disabled === disabled || - - // Check non-disabled form elements for fieldset[disabled] ancestors - "form" in elem && elem.disabled === false && ( - // Support: IE6-11+ - // Ancestry is covered for us - elem.isDisabled === disabled || - - // Otherwise, assume any non-