Started testing pluggable views

openflexure_microscope/api/app.py

@@ -0,0 +1,187 @@
+#!/usr/bin/env python
+
+from pprint import pprint
+from importlib import import_module
+import time
+import datetime
+
+from flask import (
+    Flask, render_template, Response,
+    redirect, request, jsonify, send_file)
+
+import numpy as np
+
+from openflexure_microscope.camera.pi import StreamingCamera
+
+app = Flask(__name__)
+cam = StreamingCamera()
+
+
+def parse_payload(request):
+    """Convert request to JSON. Will eventually handle error-checking."""
+    # TODO: Handle invalid JSON payloads
+    state = request.get_json()
+    return state
+
+
+def gen(camera):
+    """Video streaming generator function."""
+    while True:
+        # the obtained frame is a jpeg
+        frame = camera.get_frame()
+
+        yield (b'--frame\r\n'
+               b'Content-Type: image/jpeg\r\n\r\n' + frame + b'\r\n')
+
+
+@app.route('/')
+def index():
+    """Video streaming home page."""
+    cam.start_worker()  # Start the stream
+    return render_template('index.html')
+
+
+@app.route('/stream')
+def stream():
+    """Video streaming route. Put this in the src attribute of an img tag."""
+    return Response(
+        gen(cam),
+        mimetype='multipart/x-mixed-replace; boundary=frame')
+
+
+# TODO: Be able to change the image resolution with an option
+@app.route('/capture/', methods=['GET', 'POST', 'PUT'])
+def capture():
+    """
+    POST/PUT: Capture a single image.
+    GET: Return capture status, or download latest capture.
+    """
+    if request.method == 'POST' or request.method == 'PUT':
+        state = parse_payload(request)
+        print(state)
+
+        # Handle filename argument
+        if 'filename' in state:
+            filename = state['filename']
+        else:
+            filename = None
+
+        if 'write_to_file' in state:
+            write_to_file = bool(state['write_to_file'])
+        else:
+            write_to_file = False
+
+        if 'use_video_port' in state:
+            use_video_port = bool(state['use_video_port'])
+        else:
+            use_video_port = False
+
+        if 'resize' in state:
+            resize_h = int(state['resize'])
+            resize_w = int(resize_h*(4/3))
+            resize = (resize_w, resize_h)
+        else:
+            resize = None
+
+        response = cam.capture(
+            write_to_file=write_to_file,
+            use_video_port=use_video_port,
+            filename=filename,
+            resize=resize)
+
+        return str(response) + "\n"
+
+    else:  # If GET request
+
+        download = request.args.get('download')
+
+        state = cam.state
+
+        if ((
+                download == 'true' or
+                download == 'True' or
+                download == '1') and
+                cam.image is not None):
+
+            return send_file(cam.image.data, mimetype='image/jpeg')
+        else:
+            return jsonify(state)
+
+
+@app.route('/record/', methods=['GET', 'POST', 'PUT'])
+def record():
+    """
+    POST/PUT: Start or stop a video recording.
+    GET: Return recording status, or download latest recording
+    """
+    if request.method == 'POST' or request.method == 'PUT':
+        state = request.get_json()
+        print(state)
+
+        # Handle filename argument
+        if 'filename' in state:
+            filename = state['filename']
+        else:
+            filename = None
+
+        # Handle status argument
+        if 'status' in state:
+            status = bool(state['status'])
+
+        # synchronise the arduino_time
+        if status is True:
+            response = cam.start_recording(filename=filename)
+            return str(response)
+
+        elif status is False:
+            response = cam.stop_recording()
+            return str(response)
+
+    else:
+        download = request.args.get('download')
+
+        state = cam.state
+
+        if ((
+                download == 'true' or
+                download == 'True' or
+                download == '1') and
+                cam.state['recent_video'] is not None):
+
+            return send_file(
+                cam.state['recent_video'],
+                mimetype='video/H264',
+                as_attachment=True)
+        else:
+            return jsonify(state)
+
+
+@app.route('/preview/', methods=['GET', 'POST', 'PUT'])
+def preview():
+    """
+    POST/PUT: Start or stop the direct-to-GPU camera preview on the Pi.
+
+    GET: Return preview status
+    """
+    if request.method == 'POST' or request.method == 'PUT':
+        state = request.get_json()
+        print(state)
+
+        if 'status' in state:
+            status = bool(state['status'])
+
+        if status is False:
+            response = cam.stop_preview()
+        else:
+            response = cam.start_preview()
+
+        return str(response)
+
+    else:
+        # Get args passed via URL (not useful here. Just for reference.)
+        state = cam.state
+        return jsonify(state)
+
+
+if __name__ == '__main__':
+    app.run(host='0.0.0.0', threaded=True, debug=True, use_reloader=False)

openflexure_microscope/api/doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = openflexure_microscope_api
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

openflexure_microscope/api/doc/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=openflexure_microscope_api
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

openflexure_microscope/api/doc/requirements.txt

@@ -0,0 +1,3 @@
+Sphinx
+sphinxcontrib-httpdomain
+sphinx_rtd_theme

openflexure_microscope/api/doc/source/conf.py

@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'openflexure_microscope_api'
+copyright = '2018, Joel Collins'
+author = 'Joel Collins'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.ifconfig',
+    'sphinxcontrib.httpdomain',
+    'sphinxcontrib.autohttp.flask',
+    'sphinxcontrib.autohttp.flaskqref',
+]
+
+# Override ordering
+autodoc_member_order = 'bysource'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'openflexure_microscope_apidoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'openflexure_microscope_api.tex', 'openflexure\\_microscope\\_api Documentation',
+     'Joel Collins', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'openflexure_microscope_api', 'openflexure_microscope_api Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'openflexure_microscope_api', 'openflexure_microscope_api Documentation',
+     author, 'openflexure_microscope_api', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

openflexure_microscope/api/doc/source/index.rst

@@ -0,0 +1,36 @@
+.. openflexure_microscope_api documentation master file, created by
+   sphinx-quickstart on Thu Nov 15 11:08:18 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+OpenFlexure Microscope API
+======================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+
+API Documentation
+=================
+
+Summary
+-------
+.. qrefflask:: openflexure_microscope.api.v1:app
+   :undoc-static:
+
+API Details
+-----------
+
+.. autoflask:: openflexure_microscope.api.v1:app
+  :undoc-static:

openflexure_microscope/api/templates/index.html

@@ -0,0 +1,9 @@
+<html>
+  <head>
+    <title>Video Streaming Demonstration</title>
+  </head>
+  <body>
+    <h1>Video Streaming Demonstration</h1>
+    <img src="{{ url_for('stream') }}">
+  </body>
+</html>

openflexure_microscope/api/v1.py

@@ -17,6 +17,7 @@ from flask import (
     redirect, request, jsonify, send_file, abort,
     make_response)
 
+from flask.views import MethodView
 
 import numpy as np
 
@@ -29,21 +30,22 @@ from openflexure_stage import OpenFlexureStage
 import logging, sys
 logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
 
+logging.info("Creating StreamingCamera")
+cam = StreamingCamera()
+logging.info("Creating stage")
+stage = OpenFlexureStage("/dev/ttyUSB0")
 
 # Create the microscope object globally (common to all spawned server threads)
+logging.info("Creating microscope")
 microscope = Microscope(
-    StreamingCamera(), 
+    cam, 
-    OpenFlexureStage("/dev/ttyUSB0")
+    stage
 )
 
+logging.info("Creating app")
 # Create flask app
 app = Flask(__name__)
 
-# Make errors more API friendly
-@app.errorhandler(404)
-def not_found(error):
-    return make_response(jsonify({'error': 'Not found'}), 404)
-
 # Some useful functions
 def uri(suffix, base='/api/v1'):
     return base + suffix
@@ -57,6 +59,30 @@ def index():
         'index_v1.html'
     )
 
+
+##### TESTING CLASS STUFFS ######
+class MicroscopeView(MethodView):
+
+    def __init__(self, microscope_obj):
+        self.microscope_obj = microscope_obj
+
+
+class TestAPI(MicroscopeView):
+
+    def get(self):
+        """
+        Get method for my cool new MethodView
+        """
+        return jsonify(self.microscope_obj.state)
+
+    def post(self):
+        """
+        Post method for my cool new MethodView
+        """
+        return jsonify(request.get_json())
+
+app.add_url_rule('/test', view_func=TestAPI.as_view('test', microscope_obj=microscope))
+
 # Define API routes
 
 # Basic routes
@@ -84,7 +110,9 @@ def state():
 
 @app.route(uri('/position'), methods=['GET', 'POST', 'PUT'])
 def position():
-    """Set and get the microscope stage position"""
+    """
+    Set and get the microscope stage position
+    """
     global microscope
 
     if request.method == 'POST' or request.method == 'PUT':
@@ -249,5 +277,5 @@ def thumb_capture(capture_uuid):
         capture_obj.thumbnail,
         mimetype='image/jpeg')
 
-if __name__ == '__main__':
+if __name__ == "__main__":
-    app.run(host='0.0.0.0', threaded=True, debug=True, use_reloader=False)
+    app.run(host='0.0.0.0', port="5000", threaded=True, debug=True, use_reloader=False)

openflexure_microscope/microscope.py

@@ -8,7 +8,9 @@ from .camera.pi import StreamingCamera
 class Microscope(object):
     def __init__(self, camera: StreamingCamera, stage: OpenFlexureStage):
         """Create the microscope object.  The camera and stage should already be initialised."""
+        print("Assigning camera")
         self.camera = camera
+        print("Assigning stage")
         self.stage = stage
         self.stage.backlash = np.zeros(3, dtype=np.int)