Merge pull request NSLS-II-XPD#15 from CJ-Wright/waterfall_callback

Waterfall callback

.codecov.yml

@@ -0,0 +1,33 @@
+# codecov can find this file anywhere in the repo, so we don't need to clutter
+# the root folder.
+#comment: false
+
+codecov:
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  status:
+    patch:
+      default:
+        target: '80'
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+    project:
+      default: false
+      library:
+        target: auto
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+        paths: '!*/tests/.*'
+
+      tests:
+        target: 97.9%
+        paths: '*/tests/.*'
+
+flags:
+  tests:
+    paths:
+      - tests/

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+source = 
+    xpdview
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+
+exclude_lines =
+    if __name__ == '__main__':

.flake8

@@ -0,0 +1,9 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    doc/conf.py,
+    old,
+    build,
+    dist,
+max-complexity = 10

.landscape.yml

@@ -0,0 +1,3 @@
+python-targets:
+  - 3
+doc-warnings: true

.travis.yml

@@ -0,0 +1,70 @@
+language: python
+sudo: false
+env:
+  global:
+    BUILD_DOCS_BRANCH: master
+    DOCS_SUBDIR: doc/
+    TARGET_DEV_SUBDIR: bluesky/
+    HTML_SUBDIR: build/html
+    DOCS_CONDA_DEPS: "bluesky"
+    DOCS_PIP_DEPS: "tqdm"
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+    - $HOME/.cache/matplotlib
+
+services:
+  - mongodb
+addons:
+  apt:
+    sources:
+    - mongodb-3.2-precise
+    packages:
+    - mongodb-org-server
+
+python:
+  - 3.5
+before_install:
+  - git clone https://github.com/NSLS-II/nsls2-ci --branch master --single-branch ~/ci_scripts
+  - "/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -ac -screen 0 1280x1024x16"
+  - "export DISPLAY=:99.0"
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b -p ~/mc
+  - export PATH=~/mc/bin:$PATH
+  - conda update conda --yes
+  - export CONDARC=ci/condarc
+  - export MDS_HOST=localhost
+  - export MDS_DATABASE=test
+  - export MDS_TIMEZONE=US/Eastern
+  - mkdir -p /home/travis/.config/metadatastore
+  - 'echo ''port: 27017'' > /home/travis/.config/metadatastore/connection.yml'
+  - export FS_HOST=localhost
+  - export FS_DATABASE=test
+  - mkdir -p /home/travis/.config/filestore
+  - 'echo ''port: 27017'' > /home/travis/.config/filestore/connection.yml'
+
+
+install:
+  - export GIT_FULL_HASH=`git rev-parse HEAD`
+  - conda create --yes -n testenv numpy scipy flake8 matplotlib python=$TRAVIS_PYTHON_VERSION pytest coverage pip databroker ophyd historydict boltons doct pyepics super_state_machine mock xlrd scikit-beam bluesky pyFAI pyxdameraulevenshtein pyqt=4 -c lightsource2 -c conda-forge -c soft-matter
+  - source activate testenv
+  - python setup.py install
+  # Need to clean the python build directory (and other cruft) or pytest is
+  # going to find the build directory and get confused why there are two sets
+  # of every test file
+  - python -c "from filestore import utils, conf; utils.install_sentinels(conf.connection_config, 1)"
+  # make sure the sqlite file exists to avoid race conditions
+  - python -c "from bluesky.utils import get_history; get_history()"
+  - pip install codecov pytest-env python-coveralls
+  - git clean -xfd
+
+script:
+#  - coverage run run_tests.py
+#  - coverage report -m
+  - flake8 xpdview
+
+#after_success:
+#  - codecov
+#  - coveralls

setup.py

@@ -7,4 +7,8 @@
     description='Visualization Code for Beam line',
     zip_safe=False,
     url='https://github.com/chiahaoliu/xpdView.git',
-    )
+    install_requires=['numpy', 'six', 'matplotlib',
+                      # 'PyQt5', 'PyQt4',
+                      'scipy',
+                      'tifffile']
+)

xpdview/callbacks.py

@@ -0,0 +1,47 @@
+from bluesky.callbacks.broker import BrokerCallbackBase
+from .waterfall import Waterfall
+
+
+class LiveWaterfall(BrokerCallbackBase):
+    """
+    Stream 1D images in a waterfall viewer.
+
+    Parameters
+    ----------
+    x_name : str
+        field name for x dimension
+    y_name: str
+        field name for y dimension
+    db: databroker.Broker instance
+        The Broker to fill the events if events are not filled
+    units: tuple of str
+        The units for the x and y axes
+    """
+
+    def __init__(self, x_name, y_name, db=None, units=None):
+        super().__init__((x_name, y_name,), db=db)
+        self.db = db
+        self.x_name = x_name
+        self.y_name = y_name
+        self.units = units
+
+        from matplotlib.figure import Figure
+        self.fig = Figure()
+
+        self.wf = Waterfall(fig=self.fig, unit=self.units)
+        self.i = 0
+
+    def start(self, doc):
+        self.i = 0
+        self.wf.key_list.clear()
+        self.wf.int_data_list.clear()
+
+    def event(self, doc):
+        super().event(doc)
+        y = doc['data'][self.y_name]
+        x = doc['data'][self.x_name]
+        self.update((x, y))
+
+    def update(self, data):
+        self.wf.update(key_list=[self.i], int_data_list=[data])
+        self.i += 1

xpdview/one_dimensional_int.py

@@ -13,8 +13,8 @@
 ##############################################################################
 
 """
-This file will handle all of the one dimensional plotting of the lower left tile in the
-Display Window
+This file will handle all of the one dimensional plotting of the lower left
+tile in the Display Window
 """
 import warnings
 import matplotlib.pyplot as plt
@@ -27,7 +27,8 @@ class IntegrationPlot(object):
     Attributes
     ----------
     int_data_dict : dict
-        this dictionary holds the data to be plotted by the user; data must be stored as lists inside a list with the
+        this dictionary holds the data to be plotted by the user; data must be
+        stored as lists inside a list with the
         format [x_data_list, y_data_list]
     fig : object
         this needs to be a matplotlib figure
@@ -87,9 +88,9 @@ def give_plot(self, key):
         try:
             # grab corresponding data based on key
             data = self.int_data_dict[use_key]
-            x,y = data
+            x, y = data
             self.ax.plot(x, y)
-            #self.ax.hold(False)
+            # self.ax.hold(False)
             self.ax.legend([use_key[:10]])
             self.ax.autoscale()
             self.canvas.draw()

xpdview/waterfall.py

@@ -2,10 +2,12 @@
 import matplotlib.pyplot as plt
 from matplotlib.widgets import Slider
 
+
 def _normalize(self, array, max_val, min_val):
     """core function to normalize a ndarray"""
     return np.subtract(array, min_val) / np.subtract(max_val, min_val)
 
+
 class Waterfall:
     """class holds data and generate watefall plot
 
@@ -23,19 +25,31 @@ class Waterfall:
     unit : tuple, optional
         a tuple containing strings of x and y labels
     """
-    def __init__(self, fig, canvas, key_list=None, int_data_list=None,
+
+    def __init__(self, fig=None, canvas=None,
+                 key_list=None, int_data_list=None,
                  *, unit=None):
+        if int_data_list is None:
+            int_data_list = []
+        if key_list is None:
+            key_list = []
+        if not fig:
+            fig = plt.figure()
         self.fig = fig
+        if not canvas:
+            canvas = self.fig.canvas
         self.canvas = canvas
+
         # callback for showing legend
         self.canvas.mpl_connect('pick_event', self.on_plot_hover)
         self.key_list = key_list
         self.int_data_list = int_data_list
         self.ax = self.fig.add_subplot(111)
         self.unit = unit
+
         # flag to prevent update
         self.halt = False
-        # add sliders, which store informations
+        # add sliders, which store information
         y_offset_slider_ax = self.fig.add_axes([0.15, 0.95, 0.3, 0.035])
         self.y_offset_slider = Slider(y_offset_slider_ax,
                                       'y-offset', 0.0, 1.0,
@@ -63,21 +77,11 @@ def update(self, key_list=None, int_data_list=None, refresh=False):
             option to set refresh or not. default to False.
         """
         if not int_data_list:
-            print("INFO: no reduced data is feeded in, "
+            print("INFO: no reduced data was fed in, "
                   "waterfall plot can't be updated")
             self.halt = True
             self.no_int_data_plot(self.ax, self.canvas)
             return
-        # validate shape
-        array_shape_list = list(map(lambda x: np.shape(x[0]),
-                                    int_data_list))
-        array_shape_num = np.unique(array_shape_list)
-        if len(array_shape_num)> 1:
-            print("INFO: there are reduced data with different length, "
-                  "they might come from different calibrations or "
-                  "experiment setups. Please check if your data files\n"
-                  "INFO: waterfall plot won't be updated")
-            return
         # refresh list
         if refresh:
             self.key_list = []
@@ -86,13 +90,13 @@ def update(self, key_list=None, int_data_list=None, refresh=False):
         self.int_data_list.extend(int_data_list)
         # generate plot
         self.halt = False
-        self._update_plot()# use current value of x,y offset
+        self._update_plot()  # use current value of x,y offset
 
     def _adapt_data_list(self, int_data_list):
         """method to return statefull information of 1D data list"""
         x_array_list = []
         y_array_list = []
-        for x,y in int_data_list:
+        for x, y in int_data_list:
             x_array_list.append(x)
             y_array_list.append(y)
         y_max = np.max(y_array_list)
@@ -108,7 +112,7 @@ def on_plot_hover(self, event):
         """callback to show legend when click on one of curves"""
         line = event.artist
         name = line.get_label()
-        line.axes.legend([name],handlelength=0,
+        line.axes.legend([name], handlelength=0,
                          handletextpad=0, fancybox=True)
         line.figure.canvas.draw_idle()
 
@@ -122,8 +126,8 @@ def _update_plot(self, x_offset_val=None, y_offset_val=None):
             y_offset_val = self.y_offset_slider.val
         # get stateful info
         state = self._adapt_data_list(self.int_data_list)
-        x_array_list, y_array_list,\
-                y_min, y_max, y_dist, x_min, x_max, x_dist = state
+        x_array_list, y_array_list, \
+        y_min, y_max, y_dist, x_min, x_max, x_dist = state
         for ind, el in enumerate(zip(x_array_list, y_array_list)):
             x, y = el
             self.ax.plot(x + x_dist * ind * x_offset_val,
@@ -156,7 +160,7 @@ def no_int_data_plot(self, ax, canvas):
                             "by proper calibration and integration.\n"
                             "Please go to our documentation for more details:\n"
                             "http://xpdacq.github.io/quickstart.html"),
-                     ha='center', va='center', color='w',
-                     transform=ax.transAxes, size=11)
+                ha='center', va='center', color='w',
+                transform=ax.transAxes, size=11)
         ax.set_facecolor('k')
         canvas.draw_idle()