Args:
    data_dir (str): Path to reconstruction data.
    measurements (list of arrays): The measurements. These are currently used only
        for masking nan pixels.
    ignore_angles (optional, bool): Ignore the THETA/PHI pixel angles.
    ignore_sunblock (optional, bool): Ignore the (gaussian) sun mask.
    subsample (optional, int): Subsampling period.
    eleveation_weight (optional, float): Weight down the horizon.
    mask_measurement (optional, float): Mask measurements higher than this value.
    erode_mask (optional, int): Erode the mask.
    weights_color (tuple): Weight colors differently.
"""
def __init__(
        self,
        data_dir,
        indices=None,
        measurements=None,
        ignore_angles=False,
        ignore_sunblock=False,
        subsample=-1,
        elevation_weight=-1,
        mask_measurement=-1,
        erode_mask=-1,
        weights_color=(1, 1, 1),
        *args,
        **kwds):

    super(RGBSensorNetwork, self).__init__(*args, **kwds)

    with open(os.path.join(data_dir, 'export_data.pkl'), 'rb') as f:
        datas = cPickle.load(f)

    if subsample < 1:
        #
        # For some strange reason, if I don't subsample (even by 1),
        # then all shadom directions are transposed.
        #
        subsample = 1
        logging.warn("Subsampling by 1 to avoid strange bug in directions.")

    camera_ids = sorted(datas.keys())

    if indices is None:
        indices = range(len(camera_ids))

    for id_index in indices:
        cam_id = camera_ids[id_index]
        for color_channel in range(3):
            data = datas[cam_id]
            extra_data = data["extra_data"]

            if ignore_angles:
                Y_shdom, X_shdom = np.meshgrid(
                    np.linspace(-1, 1, 301),
                    np.linspace(-1, 1, 301)
                )
                PHI = math.pi + np.arctan2(Y_shdom, X_shdom)
                PSI = -math.pi + math.pi/2 * np.sqrt(X_shdom**2 + Y_shdom**2)
            else:
                PHI = data['PHI']
                PSI = data['PSI']

            #
            # Prepare the MASK (erode it if requested).
            #
            MASK = data["MASK"].astype(np.uint8)
            MASK[MASK<1] = 0
            MASK[MASK>1] = 1
            if erode_mask > 0:
                kernel = np.ones((3, 3), np.uint8)
                MASK = cv2.erode(MASK, kernel, iterations=erode_mask)
            MASK = MASK.astype(np.bool)

            SUN_MASK = data["SUN_MASK"]

            #
            # In case of forward simulation there are no measurements.
            # Use zeros to simplify the implementation of the code.
            #
            if measurements is not None:
                #
                # Mask high measurements (sun region).
                # Note:
                # The masking is done on all channels together
                # so that all channels will have the same mask.
                #
                if mask_measurement > 0:
                    values_mask = measurements[id_index] < mask_measurement
                    values_mask = values_mask.min(axis=-1)
                    MASK = MASK & values_mask

                measurement = measurements[id_index][..., color_channel]
            else:
                measurement = np.zeros_like(PHI)

            if subsample > 0:
                logging.info(
                    "Subsampling the measurements by {}".format(subsample)
                )

                #
                # Subsample the sensor smoothly.
                #
                PHI, PSI, SUN_MASK, measurement = \
                    subsampleSensor(subsample, PHI, PSI, SUN_MASK, measurement)

                #
                # The mask is sampled "not" smoothly.
                #
                MASK = MASK[::subsample, ::subsample]

            shape = PHI.shape

            self.measurements.append(measurement)
            self.shape_array.append(shape)
            self.phi_array.append(PHI)
            self.psi_array.append(PSI)
            self.x_array.append(extra_data["x"]*np.ones(shape=shape)/1000.0)
            self.y_array.append(extra_data["y"]*np.ones(shape=shape)/1000.0)
            self.z_array.append(extra_data["z"]*np.ones(shape=shape)/1000.0)

            #
            # Mask any nan values in the images.
            #
            nan_mask = ~np.isnan(measurement)
            self.mask_array.append(MASK & nan_mask)

            #
            # Scale by view angle.
            #
            if elevation_weight > 0:
                eps = 1e-8
                angle_scaling = -np.cos(PSI)
                angle_scaling[angle_scaling<eps] = eps
                angle_scaling = angle_scaling**elevation_weight
            else:
                angle_scaling = np.ones_like(PSI)

            #
            # Weight the scaling by channel.
            # This is used for putting more weights on the Blue channel in
            # hope to improve the reconstruction of the clouds.
            #
            angle_scaling = angle_scaling * weights_color[color_channel]
            if ignore_sunblock:
                self.weights_array.append(angle_scaling)
            else:
                self.weights_array.append(SUN_MASK*angle_scaling)

    #
    # SHDOM cant handle negative heights
    # move the origin to the lowest camera position
    #
    minz = np.min(map(lambda x: x.min(), self.z_array))
    self.z_array = map(lambda x: x-minz, self.z_array)

    #
    # Prepare perturbation.
    #
    if self.perturbate:
        self._prepare_camera_perturbation()

    #
    # Flatten the data arrays.
    #
    self._flatten_arrays()

    # Load measurements
    # Note:
    # I scale the measurements by the SHDOM_COEFF. Theoretically it would
    # make sense to apply this to the solarflux input to the SHDOM algorithm.
    # This would simplify handling real measurements and simulated images
    # in the same way. Practically this is less stable SHDOM wise.
    #
    measured_images = loadRGBmeasurements(
        base_path,
        scaling=radiometric_calibration[radiometric_set]
    )

#
# Initialize Cameras.
#
camera_network = RGBSensorNetwork(
    data_dir=base_path,
    indices=camera_ids,
    measurements=measured_images,
    ignore_sunblock=ignore_sunblock,
    subsample=subsample,
    elevation_weight=elevation_weight,
    weights_color=(0.5, 0.5, 2.) if args.weight_blue else (1, 1, 1)
) 	

/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/transformation_matrices.py:1899: UserWarning: failed to import module _transformations
  warnings.warn("failed to import module %s" % name)

Server cam_116L raised an error
===============================

Calling the cmd handler caused an error:
Traceback (most recent call last):
  File "C:\Users\addalin\Dropbox\cloud CT\cameranetwork\CameraNetwork\server.py", line 414, in _on_request
    answer = yield cb(*args, **kwds)
  File "C:\ProgramData\Anaconda2\envs\cn_client\lib\site-packages\tornado\gen.py", line 1055, in run
    value = future.result()
  File "C:\ProgramData\Anaconda2\envs\cn_client\lib\site-packages\tornado\concurrent.py", line 238, in result
    raise_exc_info(self._exc_info)
  File "C:\ProgramData\Anaconda2\envs\cn_client\lib\site-packages\tornado\gen.py", line 292, in wrapper
    result = func(*args, **kwargs)
  File "C:\Users\addalin\Dropbox\cloud CT\cameranetwork\CameraNetwork\server.py", line 992, in handle_seek
    timedelta_threshold=timedelta_threshold
  File "C:\Users\addalin\Dropbox\cloud CT\cameranetwork\CameraNetwork\controller.py", line 1381, in seekImageArray
    ignore_date_extrinsic
  File "C:\Users\addalin\Dropbox\cloud CT\cameranetwork\CameraNetwork\controller.py", line 1490, in preprocess_array
    img_array = self._vignetting.applyVignetting(img_array)
AttributeError: 'Controller' object has no attribute '_vignetting'

2019-10-22 19:06:28,009 [MainThread  ] [DEBUG]  sending message from:<CameraNetwork.gui.main.ServerModel object at 0x7f0808088dd0>
Traceback (most recent call last):
  File "/home/shubi/.conda/envs/cn_client/lib/python2.7/site-packages/enaml/qt/q_deferred_caller.py", line 42, in customEvent
    event.callback(*event.args, **event.kwargs)
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/gui/main.py", line 1682, in receive_message
    self.servers_dict[server_id].handle_reply(status, cmd, args, kwds)
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/gui/main.py", line 1977, in handle_reply
    cb(*args, **kwds)
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/gui/main.py", line 1993, in reply_tunnel_details
    subprocess.Popen(putty_cmd)
  File "/home/shubi/.conda/envs/cn_client/lib/python2.7/subprocess.py", line 394, in __init__
    errread, errwrite)
  File "/home/shubi/.conda/envs/cn_client/lib/python2.7/subprocess.py", line 1047, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/site-packages/scipy/ndimage/measurements.py:36: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject                                          
  from . import _ni_label
reading sources... [100%] usage                                                                                                                                                                                                                                          
WARNING: autodoc: failed to import module u'controller' from module u'CameraNetwork'; the following exception was raised:
No module named fisheye
/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/export.py:docstring of CameraNetwork.export.extraReconstructionData:10: WARNING: Unexpected indentation.
/home/shubi/PycharmProjects/cameranetwork/docs/source/index.rst:4: WARNING: toctree contains reference to nonexisting document 

ERROR:root:Error while loading past sun measurements:
Traceback (most recent call last):
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/controller.py", line 467, in loadSunMeasurements
    self.sunshader_angles_df = pd.concat(angles, axis=1, sort=True).mean(axis=1).to_frame(name='angle')
TypeError: concat() got an unexpected keyword argument 'sort'

python start_local.py -d "/home/shubi/Desktop/experiment_23_09_2019"

2019-09-04 14:00:46,922 [MainThread  ] [DEBUG]  Creating the 3D map view.
2019-09-04 14:00:46,923 [MainThread  ] [DEBUG]  Clearing 3D view.
2019-09-04 14:00:47,041 [MainThread  ] [DEBUG]  Threading the map projection.
Exception in thread Thread-2:
Traceback (most recent call last):
  File "/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/threading.py", line 754, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/gui/main.py", line 185, in createMapProjection
    alt0=alt0,
  File "/home/shubi/PycharmProjects/cameranetwork/CameraNetwork/visualization.py", line 97, in convertMapData
    lat0=lat0, lon0=lon0, h0=alt0)
  File "/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/site-packages/pymap3d/math/ned.py", line 225, in geodetic2ned
    e, n, u = geodetic2enu(lat, lon, h, lat0, lon0, h0, ell, deg=deg)
  File "/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/site-packages/pymap3d/math/enu.py", line 169, in geodetic2enu
    x1, y1, z1 = geodetic2ecef(lat, lon, h, ell, deg=deg)
  File "/home/shubi/.conda/envs/cvenv2.7/lib/python2.7/site-packages/pymap3d/math/ecef.py", line 47, in geodetic2ecef
    lat = radians(lat)
TypeError: only size-1 arrays can be converted to Python scalars

2019-09-04 14:00:47,234 [MainThread  ] [DEBUG]  Drawing the 3D Grid.
2019-09-04 14:00:47,268 [MainThread  ] [DEBUG]  Broadcasting message: array
2019-09-04 14:00:49,297 [MainThread  ] [INFO ]  Creating new item for server 236
2019-09-04 14:00:49,308 [MainThread  ] [DEBUG]  32.775776 35.024963 229.0 2019-09-04 11:00:47.363374
2019-09-04 14:00:49,309 [MainThread  ] [DEBUG]  Sun altitude 58:09:51.2, azimuth 221:02:47.7 at time 2019-09-04 11:00:47.363374
2019-09-04 14:00:49,309 [MainThread  ] [DEBUG]  32.775776 35.024963 229.0 2019-09-04 11:00:47.363374
2019-09-04 14:00:49,309 [MainThread  ] [DEBUG]  Sun altitude 58:09:51.2, azimuth 221:02:47.7 at time 2019-09-04 11:00:47.363374
Creating default grid 2D
Updating the GRID_ECEF
2019-09-04 14:00:49,320 [MainThread  ] [INFO ]  Adding new view of server 236
2019-09-04 14:00:49,658 [MainThread  ] [DEBUG]  Initializing the sun position: [[115.53807505 110.35075685]].
2019-09-04 14:00:49,661 [MainThread  ] [DEBUG]  Arrays LOS updated. Will update the map.
2019-09-04 14:00:49,662 [MainThread  ] [DEBUG]  Creating the LOS vectors.
2019-09-04 14:01:10,691 [MainThread  ] [INFO ]  Calculating LOS.
2019-09-04 14:01:10,692 [MainThread  ] [DEBUG]  Arrays LOS updated. Will update the map.

/home/shubi/.conda/envs/cn_client_pd_fix3/lib/python2.7/site-packages/sklearn/base.py:253: UserWarning: Trying to unpickle estimator LinearRegression from version pre-0.18 when using version 0.20.3. This might lead to breaking code or invalid results. Use at your own risk.
  UserWarning)

Traceback (most recent call last):
  File "/VISL2_net/addalin/code/cameranetwork/CameraNetwork/controller.py", line 216, in __init__
    self.sky_mask_base = sio.loadmat(gs.MASK_PATH)['mask_base']
  File "/home/addalin/anaconda2/envs/cn_client/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 208, in loadmat
    matfile_dict = MR.get_variables(variable_names)
  File "/home/addalin/anaconda2/envs/cn_client/lib/python2.7/site-packages/scipy/io/matlab/mio5.py", line 292, in get_variables
    res = self.read_var_array(hdr, process)
  File "/home/addalin/anaconda2/envs/cn_client/lib/python2.7/site-packages/scipy/io/matlab/mio5.py", line 252, in read_var_array
    return self._matrix_reader.array_from_header(header, process)
  File "mio5_utils.pyx", line 675, in scipy.io.matlab.mio5_utils.VarReader5.array_from_header
  File "mio5_utils.pyx", line 705, in scipy.io.matlab.mio5_utils.VarReader5.array_from_header
  File "mio5_utils.pyx", line 778, in scipy.io.matlab.mio5_utils.VarReader5.read_real_complex
  File "mio5_utils.pyx", line 450, in scipy.io.matlab.mio5_utils.VarReader5.read_numeric
  File "mio5_utils.pyx", line 355, in scipy.io.matlab.mio5_utils.VarReader5.read_element
  File "streams.pyx", line 195, in scipy.io.matlab.streams.ZlibInputStream.read_string
  File "streams.pyx", line 188, in scipy.io.matlab.streams.ZlibInputStream.read_into
IOError: could not read bytes
ERROR:root:None

/docs$ make latexpdf
Running Sphinx v1.8.5

Extension error:
Could not import extension numfig (exception: No module named numfig)


/docs$ make html
Running Sphinx v1.8.5

Extension error:
Could not import extension numfig (exception: No module named numfig)
Makefile:19: recipe for target 'html' failed
make: *** [html] Error 2

    # 'numfig',

Server 236 raised an error
==========================

Calling the cmd handler caused an error:
Traceback (most recent call last):
  File "/home/odroid/code/cameranetwork/CameraNetwork/server.py", line 414, in _on_request
    answer = yield cb(*args, **kwds)
  File "/usr/local/lib/python2.7/dist-packages/tornado/gen.py", line 1133, in run
    value = future.result()
  File "/usr/local/lib/python2.7/dist-packages/tornado/concurrent.py", line 261, in result
    raise_exc_info(self._exc_info)
  File "/usr/local/lib/python2.7/dist-packages/tornado/gen.py", line 307, in wrapper
    result = func(*args, **kwargs)
  File "/home/odroid/code/cameranetwork/CameraNetwork/server.py", line 1305, in handle_local_ip
    ip = re.compile('inet addr:([\d.]+)').search(eth0).group(1)
AttributeError: 'NoneType' object has no attribute 'group'