text: '''
  clean.py: functions for pixel scrubbing
  
  Copyright (c) 2017-2018 Vanessa Sochat
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.
  '''
  
  from deid.config import DeidRecipe
  from deid.logger import bot
  from deid.utils import get_temporary_name
  from pydicom import read_file
  import matplotlib
  matplotlib.use('pdf')
  import os
  import re
  
  bot.level = 3
  
  class DicomCleaner():
      '''take an input dicom file, check for burned pixels, and then clean,
         with option to save / output in multiple formats. This object should
         map to one dicom file, and the usage flow is the following:
  
         cleaner = DicomCleaner()
         summary = cleaner.detect(dicom_file)
        
         cleaner.clean()
      '''
      
      def __init__(self, output_folder=None,
                         add_padding=False,
                         margin=3,
                         deid=None,
                         font=None,
                         force=True):
  
          if output_folder is None:
              output_folder = get_temporary_name(prefix="clean")
  
          if font is None:
              font = self.default_font()
          self.font = font
          self.cmap = 'gray'
          self.output_folder = output_folder
          self.recipe = DeidRecipe(deid)
          self.results = None
          self.force = force
  
      def default_font(self):
          '''define the font style for saving png figures
             if a title is provided
          '''
          return {'family': 'serif',
                  'color':  'darkred',
                  'weight': 'normal',
                  'size': 16}
  
      def detect(self, dicom_file):
          '''detect will initiate the cleaner for a new dicom file.
          '''
          from deid.dicom.pixels.detect import has_burned_pixels
          self.results = has_burned_pixels(dicom_file, 
                                           deid=self.recipe.deid,
                                           force=self.force)
          self.dicom_file = dicom_file
          return self.results
          
  
      def clean(self):
          '''
          take a dicom image and a list of pixel coordinates, and return
          a cleaned file (if output file is specified) or simply plot 
          the cleaned result (if no file is specified)
      
          Parameters
          ==========
              add_padding: add N=margin pixels of padding
              margin: pixels of padding to add, if add_padding True
          '''
  
          if not self.results:
              bot.warning('Use %s.detect() to find coordinates first.' %self)
  
          else:
              bot.info('Scrubbing %s.' %self.dicom_file)
  
              # Load in dicom file, and image data
              dicom = read_file(self.dicom_file, force=True)
  
              # We will set original image to image, cleaned to clean
              self.original = dicom._get_pixel_array()
              self.cleaned = self.original.copy()
  
              # Compile coordinates from result
              coordinates = []
              for item in self.results['results']:
                  if len(item['coordinates']) > 0:
                      for coordinate_set in item['coordinates']:
                          # Coordinates expected to be list separated by commas
                          new_coordinates = [int(x) for x in coordinate_set.split(',')]
                          coordinates.append(new_coordinates) # [[1,2,3,4],...[1,2,3,4]]
  
              for coordinate in coordinates:
                  minr, minc, maxr, maxc = coordinate
                  self.cleaned[minc:maxc, minr:maxr] = 0  # should fill with black
                                             
  
      def get_figure(self, show=False, image_type="cleaned", title=None):
          '''get a figure for an original or cleaned image. If the image
             was already clean, it is simply a copy of the original.
             If show is True, plot the image.
          '''
          from matplotlib import pyplot as plt
          
          if hasattr(self, image_type):
              fig, ax = plt.subplots(figsize=(10, 6))      
              ax.imshow(self.cleaned, cmap=self.cmap)
              if title is not None:
                  plt.title(title, fontdict=self.font)
              if show is True:
                  plt.show()
              return plt
  
  
      def _get_clean_name(self, output_folder, extension='dcm'):
          '''return a full path to an output file, with custom folder and
             extension. If the output folder isn't yet created, make it.
   
             Parameters
             ==========
             output_folder: the output folder to create, will be created if doesn't
             exist.
             extension: the extension of the file to create a name for, should
             not start with "."
          '''
          if output_folder is None:
              output_folder = self.output_folder
  
          if not os.path.exists(output_folder):
              bot.debug('Creating output folder %s' % output_folder)
              os.mkdir(output_folder)
  
          basename = re.sub('[.]dicom|[.]dcm', '', os.path.basename(self.dicom_file))
          return "%s/cleaned-%s.%s" %(output_folder, basename, extension)
  
      def save_png(self, output_folder=None, image_type="cleaned", title=None):
          '''save an original or cleaned dicom as png to disk.
             Default image_format is "cleaned" and can be set 
             to "original." If the image was already clean (not 
             flagged) the cleaned image is just a copy of original
          '''
          from matplotlib import pyplot as plt
  
          if hasattr(self, image_type):
              png_file = self._get_clean_name(output_folder, 'png')
              plt = self.get_figure(image_type=image_type, title=title)
              plt.savefig(png_file)
              plt.close()
              return png_file
          else:
              bot.warning('use detect() --> clean() before saving is possible.')
  
  
      def save_dicom(self, output_folder=None, image_type="cleaned"):
          '''save a cleaned dicom to disk. We expose an option to save
             an original (change image_type to "original" to be consistent,
             although this is not incredibly useful given it would duplicate
             the original data.
          '''
          # Having clean also means has dicom image
          if hasattr(self, image_type):
              dicom_name = self._get_clean_name(output_folder)
              dicom = read_file(self.dicom_file,force=True)
              # If going from compressed, change TransferSyntax
              if dicom.file_meta.TransferSyntaxUID.is_compressed is True:
                  dicom.decompress()
              dicom.PixelData = self.cleaned.tostring()
              dicom.save_as(dicom_name)
              return dicom_name
          else:
              bot.warning('use detect() --> clean() before saving is possible.')
  