adding pixel examples

MANIFEST.in

@@ -1,6 +1,7 @@
 include README.md LICENSE
 recursive-include deid *
 recursive-exclude * __pycache__
+recursive-exclude * app
 recursive-exclude * *.pyc
 recursive-exclude * *.pyo
 recursive-exclude * *.orig

deid/dicom/__init__.py

@@ -12,7 +12,6 @@
 from .fields import  extract_sequence
 
 from .pixels import (
-    clean_pixels,
     has_burned_pixels,
-    has_burned_pixels_single
+    DicomCleaner
 )

deid/dicom/pixels/__init__.py

@@ -0,0 +1,2 @@
+from .detect import has_burned_pixels
+from .clean import DicomCleaner

deid/dicom/pixels/clean.py

@@ -0,0 +1,149 @@
+'''
+clean.py: functions for pixel scrubbing
+
+Copyright (c) 2017 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.logger import bot
+from pydicom import read_file
+import tempfile
+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):
+
+        if output_folder is None:
+            output_folder = tempfile.mkdtemp()
+
+        self.output_folder = output_folder
+        self.deid = deid
+        self.results = None
+
+    def detect(self, dicom_file):
+        '''detect will initiate the cleaner for a new dicom file.
+        '''
+        from .detect import has_burned_pixels
+        self.results = has_burned_pixels(dicom_file)
+        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)
+
+        elif self.results['flagged'] is False:
+            bot.info('Image was not flagged, nothing to clean.' %self)
+
+        else:
+            bot.info('Cleaning %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.image = dicom._get_pixel_array()
+            self.clean = self.image.copy()
+
+            # Compile coordinates from result
+            coordinates = []
+            for item in self.results['results']:
+                if len(item['coordinates']) > 0:
+                    coordinates.append(item['coordinates']) # [[1,2,3,4],...[1,2,3,4]]
+
+            print("Blanking %s coordinate boxes" %(len(coordinates)))
+            for coordinate in coordinates:
+                minr, minc, maxr, maxc = coordinate
+                self.clean[minr:maxr, minc:maxc] = 0  # should fill with black
+
+
+    def get_figure(self, show=False):
+        '''get a figure for a cleaned image, if exists.'''
+        from matplotlib import pyplot as plt
+        plt = None
+
+        if hasattr(self,"clean"):
+            fig, ax = plt.subplots(figsize=(10, 6))        
+            ax.imshow(self.clean)
+            if show is True:
+                plt.show()
+        return plt
+
+
+    def _get_clean_name(self, extension='dcm'):
+        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):
+        '''save a cleaned dicom as png to disk'''
+        from matplotlib import pyplot as plt
+
+        if output_folder is None:
+            output_folder = self.output_folder
+
+        if hasattr(self,"clean"):
+            png_file = self._get_clean_name('png')
+            fig, ax = plt.subplots(figsize=(10, 6))        
+            ax.imshow(self.clean)
+            plt.savefig(png_file)
+
+
+    def save_dicom(self, output_folder=None):
+        '''save a cleaned dicom to disk'''
+        if output_folder is None:
+            output_folder = self.output_folder
+
+        # Having clean also means has dicom image
+        if hasattr(self,"clean"):
+            dicom_name = self._get_clean_name()
+            dicom = read_file(self.dicom_file,force=True)
+            dicom.PixelData = self.clean.tostring()
+            dicom.save_as(dicom_name)
+            return dicom_name
+        else:
+            bot.warning('use detect() --> clean() before saving clean is possible.')