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2019-07-14libcamera: buffer: Split memory information to BufferMemoryLaurent Pinchart
The Buffer class is a large beast the stores information about the buffer memory, dynamic metadata related to the frame stored in the buffer, and buffer reference data (in the index). In order to implement buffer import we will need to extend this with dmabuf file descriptors, making usage of the class even more complex. Refactor the Buffer class by splitting the buffer memory information to a BufferMemory class, and repurposing the Buffer class to reference a buffer and to store dynamic metadata. The BufferMemory class becomes a long term storage, valid and stable from the time buffer memory is allocated to the time it is freed. The Buffer class, on the other hand, becomes transient, is created on demand when an application requires a buffer, is given to a request, and is deleted when the request completes. Buffer and BufferMemory don't need to be copied, so their copy constructor and assignment operators are deleted. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se>
2019-06-11test: camera: Increase runtime for capture testNiklas Söderlund
Upstream commit 2978a505aaa981b2 ("media: vimc: stream: fix thread state before sleep") changes the frame rate when capturing from the vimc raw capture video nodes. The commit changes the frame rate from thousands of frames per second to to roughly fifty. The libcamera capture test was written with the assumption that vimc would keep providing this fast frame rate and ran for a very short time to decrease the overall run time of tests. This is no longer possible and the test fails as it can't capture enough frames in its runtime, increase the runtime to match the new vimc frame rate. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com>
2019-06-10test: camera: Fix initialisationKieran Bingham
Three tests {capture,configuration_set,statemachine} override the CameraTest::init() function, and call it as the first action. However they were not checking the return value, and each of the tests will segfault if the VIMC camera is not obtained. Check the return value of the CameraTest base class initialisation and return any errors to the test suite if initialisation fails. Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Signed-off-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
2019-05-23meson: Create and use a dependency for libcamera and its headersLaurent Pinchart
Instead of manually adding the libcamera library and include path to every target that requires it, declare a dependency that groups the headers as source, the library and the include path, and use it through the project. This simplifies handling of the dependency. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
2019-05-23meson: Fix coding style in meson.build filesLaurent Pinchart
Consistently go for 4 spaces indentation, and always put a space between the colon in argument lists, as per the examples from the meson documentation. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com>
2019-05-23libcamera: camera: Add a validation API to the CameraConfiguration classLaurent Pinchart
The CameraConfiguration class implements a simple storage of StreamConfiguration with internal validation limited to verifying that the stream configurations are not empty. Extend this mechanism by implementing a smart validate() method backed by pipeline handlers. This new mechanism changes the semantic of the camera configuration. The Camera::generateConfiguration() operation still generates a default configuration based on roles, but now also supports generating empty configurations to be filled by applications. Applications can inspect the configuration, optionally modify it, and validate it. The validation implements "try" semantics and adjusts invalid configurations instead of rejecting them completely. Applications then decide whether to accept the modified configuration, or try again with a different set of parameters. Once the configuration is valid, it is passed to Camera::configure(), and pipeline handlers are guaranteed that the configuration they receive is valid. A reference to the Camera may need to be stored in the CameraConfiguration derived classes in order to access it from their validate() implementation. This must be stored as a std::shared_ptr<> as the CameraConfiguration instances belong to applications. In order to make this possible, make the Camera class inherit from std::shared_from_this<>. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se>
2019-05-23libcamera: camera: Return a pointer from generateConfiguration()Laurent Pinchart
To prepare for specialising the CameraConfiguration class in pipeline handlers, return a pointer to a camera configuration instead of a reference from Camera::generateConfiguration(). The camera configuration always needs to be allocated from the pipeline handler, and its ownership is passed to the application. For symmetry, change Camera::configure() to take a CameraConfiguration pointer instead of a reference. This aligns with our coding practice of passing parameters that are modified by the callee by pointer. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-05-23libcamera: Refactor the camera configuration storage and APILaurent Pinchart
Refactor the CameraConfiguration structure to not rely on Stream instances. This is a step towards making the camera configuration object more powerful with configuration validation using "try" semantics. The CameraConfiguration now exposes a simple vector-like API to access the contained stream configurations. Both operator[]() and at() are provided to access elements. The isEmpty() method is renamed to empty() and the methods reordered to match the std::vector class. As applications need access to the Stream instances associated with the configuration entries in order to associate buffers with streams when creating requests, expose the stream selected by the pipeline handler through a new StreamConfiguration::stream(). Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-05-23libcamera: Use stream roles directly instead of StreamUsageLaurent Pinchart
In order to prepare for an API overhall of the camera configuration generation, remove the StreamUsage class and replace its uses by stream roles. The size hints can't be specified anymore, and will be replaced with an API on the StreamConfiguration to negotiate configuration parameters with cameras. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-05-23libcamera: camera: Rename configureStreams() and streamConfiguration()Laurent Pinchart
Rename the configureStreams() and streamConfiguration() methods to configure() and generateConfiguration() respectively in order to clarify the API. Both methods deal with CameraConfiguration objects, and are thus not limited to streams, even if a CameraConfiguration currently contains streams only. While at it, remove the qcam MainWindow::configureStreams() method that is declared but never defined or used. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-04-30test: Unify naming of configurations in testsLaurent Pinchart
Name all instances of CameraConfiguration "config", and all instances of StreamConfiguration "cfg" accross all tests. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se>
2019-04-30libcamera: Use the Size class through libcameraLaurent Pinchart
Several of our structures include width and height fields that model a size while we have a Size class for that purpose. Use the Size class through libcamera, and give it a toString() method like other geometry and format classes. Signed-off-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Niklas Söderlund <niklas.soderlund@ragnatech.se>
2019-04-09libcamera: Switch to CameraConfigurationNiklas Söderlund
Implement the camera configuration thru out the library, tests, cam and qcam tools. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com>
2019-04-05libcamera: camera: Add support for stream usagesNiklas Söderlund
Instead of requesting the default configuration for a set of streams where the application has to figure out which streams provided by the camera is best suited for its intended usage, have the library figure this out by using stream usages. The application asks the library for a list of streams and a suggested default configuration for them by supplying a list of stream usages. Once the list is retrieved the application can fine-tune the returned configuration and then try to apply it to the camera. Currently no pipeline handler is prepared to handle stream usages but nor did it make use of the list of Stream IDs which was the previous interface. The main reason for this is that all cameras currently only provide one stream each. This will still be the case but the API will be prepared to expand both pipeline handlers and applications to support streams usages. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com>
2019-04-04test: camera: Remove test for bad Stream IDsNiklas Söderlund
In preparation of reworking how a default configuration is retrieved from a camera remove test that stream IDs must be valid as the data type passed to Camera::streamConfiguration() will change. This change is in preparation for an invasive change. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-04-04test: camera: Remove streams argument from configurationValid()Niklas Söderlund
In preparation of reworking how a default configuration is retrieved from a camera remove the streams and validation using the stream when judging if a camera configuration is valid. This is needed as once stream usage hints are added applications will no longer fetch default configuration based on Stream IDs so using them to verify the returned format is not useful. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Jacopo Mondi <jacopo@jmondi.org>
2019-03-14test: camera: Add state machine testNiklas Söderlund
Add a test of the different access level enforced by the state machine inside the camera. The state machine aims to limit operations on the camera to the cameras state. The test exercises all states of the camera and verifies that only the intended operations are possible at each stage. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
2019-03-14test: camera: Add capture testNiklas Söderlund
Correctly configure the camera using the default configuration and run a capture session for 100 milliseconds, which is plenty of time, in tests over 600 requests completed using the vimc pipeline. The test passes if at least the number of buffers used in the capture times two number of requests completes to prove we cycle through all buffers. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
2019-03-14test: camera: Add setting of configuration testNiklas Söderlund
Try to set the default configuration, a modified valid configuration and an invalid configuration. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
2019-03-14test: camera: Add read default configuration testNiklas Söderlund
Add a test to verify reading the default configuration from a camera works. Signed-off-by: Niklas Söderlund <niklas.soderlund@ragnatech.se> Reviewed-by: Laurent Pinchart <laurent.pinchart@ideasonboard.com> Reviewed-by: Kieran Bingham <kieran.bingham@ideasonboard.com>
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#!/usr/bin/env python3
#
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (C) 2019, Raspberry Pi (Trading) Limited
#
# ctt.py - camera tuning tool

import os
import sys
from ctt_image_load import *
from ctt_ccm import *
from ctt_awb import *
from ctt_alsc import *
from ctt_lux import *
from ctt_noise import *
from ctt_geq import *
from ctt_pretty_print_json import *
import random
import json
import re

"""
This file houses the camera object, which is used to perform the calibrations.
The camera object houses all the calibration images as attributes in two lists:
    - imgs (macbeth charts)
    - imgs_alsc (alsc correction images)
Various calibrations are methods of the camera object, and the output is stored
in a dictionary called self.json.
Once all the caibration has been completed, the Camera.json is written into a
json file.
The camera object initialises its json dictionary by reading from a pre-written
blank json file. This has been done to avoid reproducing the entire json file
in the code here, thereby avoiding unecessary clutter.
"""


"""
Get the colour and lux values from the strings of each inidvidual image
"""
def get_col_lux(string):
    """
    Extract colour and lux values from filename
    """
    col = re.search(r'([0-9]+)[kK](\.(jpg|jpeg|brcm|dng)|_.*\.(jpg|jpeg|brcm|dng))$', string)
    lux = re.search(r'([0-9]+)[lL](\.(jpg|jpeg|brcm|dng)|_.*\.(jpg|jpeg|brcm|dng))$', string)
    try:
        col = col.group(1)
    except AttributeError:
        """
        Catch error if images labelled incorrectly and pass reasonable defaults
        """
        return None, None
    try:
        lux = lux.group(1)
    except AttributeError:
        """
        Catch error if images labelled incorrectly and pass reasonable defaults
        Still returns colour if that has been found.
        """
        return col, None
    return int(col), int(lux)


"""
Camera object that is the backbone of the tuning tool.
Input is the desired path of the output json.
"""
class Camera:
    def __init__(self, jfile):
        self.path = os.path.dirname(os.path.expanduser(__file__)) + '/'
        if self.path == '/':
            self.path = ''
        self.imgs = []
        self.imgs_alsc = []
        self.log = 'Log created : ' + time.asctime(time.localtime(time.time()))
        self.log_separator = '\n'+'-'*70+'\n'
        self.jf = jfile
        """
        initial json dict populated by uncalibrated values
        """
        self.json = {
            "rpi.black_level": {
                "black_level": 4096
            },
            "rpi.dpc": {
            },
            "rpi.lux": {
                "reference_shutter_speed": 10000,
                "reference_gain": 1,
                "reference_aperture": 1.0
            },
            "rpi.noise": {
            },
            "rpi.geq": {
            },
            "rpi.sdn": {
            },
            "rpi.awb": {
                "priors": [
                    {"lux": 0, "prior": [2000, 1.0, 3000, 0.0, 13000, 0.0]},
                    {"lux": 800, "prior": [2000, 0.0, 6000, 2.0, 13000, 2.0]},
                    {"lux": 1500, "prior": [2000, 0.0, 4000, 1.0, 6000, 6.0, 6500, 7.0, 7000, 1.0, 13000, 1.0]}
                ],
                "modes": {
                    "auto": {"lo": 2500, "hi": 8000},
                    "incandescent": {"lo": 2500, "hi": 3000},
                    "tungsten": {"lo": 3000, "hi": 3500},
                    "fluorescent": {"lo": 4000, "hi": 4700},
                    "indoor": {"lo": 3000, "hi": 5000},
                    "daylight": {"lo": 5500, "hi": 6500},
                    "cloudy": {"lo": 7000, "hi": 8600}
                },
                "bayes": 1
            },
            "rpi.agc": {
                "metering_modes": {
                    "centre-weighted": {
                        "weights": [3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 0, 0, 0, 0]
                    },
                    "spot": {
                        "weights": [2, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
                    },
                    "matrix": {
                        "weights": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
                    }
                },
                "exposure_modes": {
                    "normal": {
                        "shutter": [100, 10000, 30000, 60000, 120000],
                        "gain": [1.0, 2.0, 4.0, 6.0, 6.0]
                    },
                    "sport": {
                        "shutter": [100, 5000, 10000, 20000, 120000],
                        "gain": [1.0, 2.0, 4.0, 6.0, 6.0]
                    }
                },
                "constraint_modes": {
                    "normal": [
                        {"bound": "LOWER", "q_lo": 0.98, "q_hi": 1.0, "y_target": [0, 0.5, 1000, 0.5]}
                    ],
                    "highlight": [
                        {"bound": "LOWER", "q_lo": 0.98, "q_hi": 1.0, "y_target": [0, 0.5, 1000, 0.5]},
                        {"bound": "UPPER", "q_lo": 0.98, "q_hi": 1.0, "y_target": [0, 0.8, 1000, 0.8]}
                    ]
                },
                "y_target": [0, 0.16, 1000, 0.165, 10000, 0.17]
            },
            "rpi.alsc": {
                'omega': 1.3,
                'n_iter': 100,
                'luminance_strength': 0.7,
            },
            "rpi.contrast": {
                "ce_enable": 1,
                "gamma_curve": [
                    0,     0,
                    1024,  5040,
                    2048,  9338,
                    3072,  12356,
                    4096,  15312,
                    5120,  18051,
                    6144,  20790,
                    7168,  23193,
                    8192,  25744,
                    9216,  27942,
                    10240, 30035,
                    11264, 32005,
                    12288, 33975,
                    13312, 35815,
                    14336, 37600,
                    15360, 39168,
                    16384, 40642,
                    18432, 43379,
                    20480, 45749,
                    22528, 47753,
                    24576, 49621,
                    26624, 51253,
                    28672, 52698,
                    30720, 53796,
                    32768, 54876,
                    36864, 57012,
                    40960, 58656,
                    45056, 59954,
                    49152, 61183,
                    53248, 62355,
                    57344, 63419,
                    61440, 64476,
                    65535, 65535
                ]
            },
            "rpi.ccm": {
            },
            "rpi.sharpen": {
            }
        }

    """
    Perform colour correction calibrations by comparing macbeth patch colours
    to standard macbeth chart colours.
    """
    def ccm_cal(self, do_alsc_colour):
        if 'rpi.ccm' in self.disable:
            return 1
        print('\nStarting CCM calibration')
        self.log_new_sec('CCM')
        """
        if image is greyscale then CCm makes no sense
        """
        if self.grey:
            print('\nERROR: Can\'t do CCM on greyscale image!')
            self.log += '\nERROR: Cannot perform CCM calibration '
            self.log += 'on greyscale image!\nCCM aborted!'
            del self.json['rpi.ccm']
            return 0
        a = time.time()
        """
        Check if alsc tables have been generated, if not then do ccm without
        alsc
        """
        if ("rpi.alsc" not in self.disable) and do_alsc_colour:
            """
            case where ALSC colour has been done, so no errors should be
            expected...
            """
            try:
                cal_cr_list = self.json['rpi.alsc']['calibrations_Cr']
                cal_cb_list = self.json['rpi.alsc']['calibrations_Cb']
                self.log += '\nALSC tables found successfully'
            except KeyError:
                cal_cr_list, cal_cb_list = None, None
                print('WARNING! No ALSC tables found for CCM!')
                print('Performing CCM calibrations without ALSC correction...')
                self.log += '\nWARNING: No ALSC tables found.\nCCM calibration '
                self.log += 'performed without ALSC correction...'
        else:
            """
            case where config options result in CCM done without ALSC colour tables
            """
            cal_cr_list, cal_cb_list = None, None
            self.log += '\nWARNING: No ALSC tables found.\nCCM calibration '
            self.log += 'performed without ALSC correction...'

        """
        Do CCM calibration
        """
        try:
            ccms = ccm(self, cal_cr_list, cal_cb_list)
        except ArithmeticError:
            print('ERROR: Matrix is singular!\nTake new pictures and try again...')
            self.log += '\nERROR: Singular matrix encountered during fit!'
            self.log += '\nCCM aborted!'
            return 1
        """
        Write output to json
        """
        self.json['rpi.ccm']['ccms'] = ccms
        self.log += '\nCCM calibration written to json file'
        print('Finished CCM calibration')

    """
    Auto white balance calibration produces a colour curve for
    various colour temperatures, as well as providing a maximum 'wiggle room'
    distance from this curve (transverse_neg/pos).
    """
    def awb_cal(self, greyworld, do_alsc_colour):
        if 'rpi.awb' in self.disable:
            return 1
        print('\nStarting AWB calibration')
        self.log_new_sec('AWB')
        """
        if image is greyscale then AWB makes no sense
        """
        if self.grey:
            print('\nERROR: Can\'t do AWB on greyscale image!')
            self.log += '\nERROR: Cannot perform AWB calibration '
            self.log += 'on greyscale image!\nAWB aborted!'
            del self.json['rpi.awb']
            return 0
        """
        optional set greyworld (e.g. for noir cameras)
        """
        if greyworld:
            self.json['rpi.awb']['bayes'] = 0
            self.log += '\nGreyworld set'
        """
        Check if alsc tables have been generated, if not then do awb without
        alsc correction
        """
        if ("rpi.alsc" not in self.disable) and do_alsc_colour:
            try:
                cal_cr_list = self.json['rpi.alsc']['calibrations_Cr']
                cal_cb_list = self.json['rpi.alsc']['calibrations_Cb']
                self.log += '\nALSC tables found successfully'
            except KeyError:
                cal_cr_list, cal_cb_list = None, None
                print('ERROR, no ALSC calibrations found for AWB')
                print('Performing AWB without ALSC tables')
                self.log += '\nWARNING: No ALSC tables found.\nAWB calibration '
                self.log += 'performed without ALSC correction...'
        else:
            cal_cr_list, cal_cb_list = None, None
            self.log += '\nWARNING: No ALSC tables found.\nAWB calibration '
            self.log += 'performed without ALSC correction...'
        """
        call calibration function
        """
        plot = "rpi.awb" in self.plot
        awb_out = awb(self, cal_cr_list, cal_cb_list, plot)
        ct_curve, transverse_neg, transverse_pos = awb_out
        """
        write output to json
        """
        self.json['rpi.awb']['ct_curve'] = ct_curve
        self.json['rpi.awb']['sensitivity_r'] = 1.0
        self.json['rpi.awb']['sensitivity_b'] = 1.0
        self.json['rpi.awb']['transverse_pos'] = transverse_pos
        self.json['rpi.awb']['transverse_neg'] = transverse_neg
        self.log += '\nAWB calibration written to json file'
        print('Finished AWB calibration')

    """
    Auto lens shading correction completely mitigates the effects of lens shading for ech
    colour channel seperately, and then partially corrects for vignetting.
    The extent of the correction depends on the 'luminance_strength' parameter.
    """
    def alsc_cal(self, luminance_strength, do_alsc_colour):
        if 'rpi.alsc' in self.disable:
            return 1
        print('\nStarting ALSC calibration')
        self.log_new_sec('ALSC')
        """
        check if alsc images have been taken
        """
        if len(self.imgs_alsc) == 0:
            print('\nError:\nNo alsc calibration images found')
            self.log += '\nERROR: No ALSC calibration images found!'
            self.log += '\nALSC calibration aborted!'
            return 1
        self.json['rpi.alsc']['luminance_strength'] = luminance_strength
        if self.grey and do_alsc_colour:
            print('Greyscale camera so only luminance_lut calculated')
            do_alsc_colour = False
            self.log += '\nWARNING: ALSC colour correction cannot be done on '
            self.log += 'greyscale image!\nALSC colour corrections forced off!'
        """
        call calibration function
        """
        plot = "rpi.alsc" in self.plot
        alsc_out = alsc_all(self, do_alsc_colour, plot)
        cal_cr_list, cal_cb_list, luminance_lut, av_corn = alsc_out
        """
        write ouput to json and finish if not do_alsc_colour
        """
        if not do_alsc_colour:
            self.json['rpi.alsc']['luminance_lut'] = luminance_lut
            self.json['rpi.alsc']['n_iter'] = 0
            self.log += '\nALSC calibrations written to json file'
            self.log += '\nNo colour calibrations performed'
            print('Finished ALSC calibrations')
            return 1

        self.json['rpi.alsc']['calibrations_Cr'] = cal_cr_list
        self.json['rpi.alsc']['calibrations_Cb'] = cal_cb_list
        self.json['rpi.alsc']['luminance_lut'] = luminance_lut
        self.log += '\nALSC colour and luminance tables written to json file'

        """
        The sigmas determine the strength of the adaptive algorithm, that
        cleans up any lens shading that has slipped through the alsc. These are
        determined by measuring a 'worst-case' difference between two alsc tables
        that are adjacent in colour space. If, however, only one colour
        temperature has been provided, then this difference can not be computed
        as only one table is available.
        To determine the sigmas you would have to estimate the error of an alsc
        table with only the image it was taken on as a check. To avoid circularity,
        dfault exaggerated sigmas are used, which can result in too much alsc and
        is therefore not advised.
        In general, just take another alsc picture at another colour temperature!
        """

        if len(self.imgs_alsc) == 1:
            self.json['rpi.alsc']['sigma'] = 0.005
            self.json['rpi.alsc']['sigma_Cb'] = 0.005
            print('\nWarning:\nOnly one alsc calibration found'
                  '\nStandard sigmas used for adaptive algorithm.')
            print('Finished ALSC calibrations')
            self.log += '\nWARNING: Only one colour temperature found in '
            self.log += 'calibration images.\nStandard sigmas used for adaptive '
            self.log += 'algorithm!'
            return 1

        """
        obtain worst-case scenario residual sigmas
        """
        sigma_r, sigma_b = get_sigma(self, cal_cr_list, cal_cb_list)
        """
        write output to json
        """
        self.json['rpi.alsc']['sigma'] = np.round(sigma_r, 5)
        self.json['rpi.alsc']['sigma_Cb'] = np.round(sigma_b, 5)
        self.log += '\nCalibrated sigmas written to json file'
        print('Finished ALSC calibrations')

    """
    Green equalisation fixes problems caused by discrepancies in green
    channels. This is done by measuring the effect on macbeth chart patches,
    which ideally would have the same green values throughout.
    An upper bound linear model is fit, fixing a threshold for the green
    differences that are corrected.
    """
    def geq_cal(self):
        if 'rpi.geq' in self.disable:
            return 1
        print('\nStarting GEQ calibrations')
        self.log_new_sec('GEQ')
        """
        perform calibration
        """
        plot = 'rpi.geq' in self.plot
        slope, offset = geq_fit(self, plot)
        """
        write output to json
        """
        self.json['rpi.geq']['offset'] = offset
        self.json['rpi.geq']['slope'] = slope
        self.log += '\nGEQ calibrations written to json file'
        print('Finished GEQ calibrations')

    """
    Lux calibrations allow the lux level of a scene to be estimated by a ratio
    calculation. Lux values are used in the pipeline for algorithms such as AGC
    and AWB
    """
    def lux_cal(self):
        if 'rpi.lux' in self.disable:
            return 1
        print('\nStarting LUX calibrations')
        self.log_new_sec('LUX')
        """
        The lux calibration is done on a single image. For best effects, the
        image with lux level closest to 1000 is chosen.
        """
        luxes = [Img.lux for Img in self.imgs]
        argmax = luxes.index(min(luxes, key=lambda l: abs(1000-l)))
        Img = self.imgs[argmax]
        self.log += '\nLux found closest to 1000: {} lx'.format(Img.lux)
        self.log += '\nImage used: ' + Img.name
        if Img.lux < 50:
            self.log += '\nWARNING: Low lux could cause inaccurate calibrations!'
        """
        do calibration
        """
        lux_out, shutter_speed, gain = lux(self, Img)
        """
        write output to json
        """
        self.json['rpi.lux']['reference_shutter_speed'] = shutter_speed
        self.json['rpi.lux']['reference_gain'] = gain
        self.json['rpi.lux']['reference_lux'] = Img.lux
        self.json['rpi.lux']['reference_Y'] = lux_out
        self.log += '\nLUX calibrations written to json file'
        print('Finished LUX calibrations')

    """
    Noise alibration attempts to describe the noise profile of the sensor. The
    calibration is run on macbeth images and the final output is taken as the average
    """
    def noise_cal(self):
        if 'rpi.noise' in self.disable:
            return 1
        print('\nStarting NOISE calibrations')
        self.log_new_sec('NOISE')
        """
        run calibration on all images and sort by slope.
        """
        plot = "rpi.noise" in self.plot
        noise_out = sorted([noise(self, Img, plot) for Img in self.imgs], key=lambda x: x[0])
        self.log += '\nFinished processing images'
        """
        take the average of the interquartile
        """
        length = len(noise_out)
        noise_out = np.mean(noise_out[length//4:1+3*length//4], axis=0)
        self.log += '\nAverage noise profile: constant = {} '.format(int(noise_out[1]))
        self.log += 'slope = {:.3f}'.format(noise_out[0])
        """
        write to json
        """
        self.json['rpi.noise']['reference_constant'] = int(noise_out[1])
        self.json['rpi.noise']['reference_slope'] = round(noise_out[0], 3)
        self.log += '\nNOISE calibrations written to json'
        print('Finished NOISE calibrations')

    """
    Removes json entries that are turned off
    """
    def json_remove(self, disable):
        self.log_new_sec('Disabling Options', cal=False)
        if len(self.disable) == 0:
            self.log += '\nNothing disabled!'
            return 1
        for key in disable:
            try:
                del self.json[key]
                self.log += '\nDisabled: ' + key
            except KeyError:
                self.log += '\nERROR: ' + key + ' not found!'
    """
    writes the json dictionary to the raw json file then make pretty
    """
    def write_json(self):
        """
        Write json dictionary to file
        """
        jstring = json.dumps(self.json, sort_keys=False)
        """
        make it pretty :)
        """
        pretty_print_json(jstring, self.jf)

    """
    add a new section to the log file
    """
    def log_new_sec(self, section, cal=True):
        self.log += '\n'+self.log_separator
        self.log += section
        if cal:
            self.log += ' Calibration'
        self.log += self.log_separator

    """
    write script arguments to log file
    """
    def log_user_input(self, json_output, directory, config, log_output):
        self.log_new_sec('User Arguments', cal=False)
        self.log += '\nJson file output: ' + json_output
        self.log += '\nCalibration images directory: ' + directory
        if config is None:
            self.log += '\nNo configuration file input... using default options'
        elif config is False:
            self.log += '\nWARNING: Invalid configuration file path...'
            self.log += ' using default options'
        elif config is True:
            self.log += '\nWARNING: Invalid syntax in configuration file...'
            self.log += ' using default options'
        else:
            self.log += '\nConfiguration file: ' + config
        if log_output is None:
            self.log += '\nNo log file path input... using default: ctt_log.txt'
        else:
            self.log += '\nLog file output: ' + log_output

        # if log_output

    """
    write log file
    """
    def write_log(self, filename):
        if filename is None:
            filename = 'ctt_log.txt'
        self.log += '\n' + self.log_separator
        with open(filename, 'w') as logfile:
            logfile.write(self.log)

    """
    Add all images from directory, pass into relevant list of images and
    extrace lux and temperature values.
    """
    def add_imgs(self, directory, mac_config, blacklevel=-1):
        self.log_new_sec('Image Loading', cal=False)
        img_suc_msg = 'Image loaded successfully!'
        print('\n\nLoading images from '+directory)
        self.log += '\nDirectory: ' + directory
        """