v1.1.0 stable

api.py

@@ -3,7 +3,7 @@ import copy
 import requests
 import uuid
 from flask import Flask, request, redirect, url_for, render_template, flash, jsonify, Blueprint
-
+from give_color import get_color
 from model import Oral
 
 oral_api = Blueprint('oral', __name__)
@@ -38,7 +38,15 @@ def recognize():
                 print('' if verbose == 0 else 'verbose out:')
                 oral = Oral(finding, conclusion, verbose = False if verbose == 0 else 1)
                 data = oral.get_json()
-                return jsonify({'success': True, 'description': {'data': data}}), 200
+                finding_list, conclusion_list, findind_replaced_word, conclusion_replaced_word, ImmunohistochemistryContent, MolecularResultsContent = oral.get_entity()
+                color_finding = get_color(finding, finding_list, findind_replaced_word, ImmunohistochemistryContent,
+                                          MolecularResultsContent)
+                color_conclusion = get_color(conclusion, conclusion_list, conclusion_replaced_word,
+                                             ImmunohistochemistryContent, MolecularResultsContent)
+                return jsonify({'success': True,
+                                'description': {'entity': data,
+                                                'color': {'finding': color_finding,
+                                                          'conclusion': color_conclusion}}}), 200
             except Exception as e:
                 print("/n******ERROR SRART******/n")
                 print(e)

give_color.py

+##
+from model import Oral
+import re
+
+##
+Finding = """
+左IV区淋巴结：1枚，直径2.5cm（1）
+颏下：1枚，直径2cm（1）
+左颊：部分上、下颌骨及颊部组织12*9*8cm，黏膜切面见一肿块6*3*2cm，灰白，界不清（1）
+送检切缘：前内、前外、上内、上外、颊、翼内肌、翼外肌、腮腺、鼻底、鼻旁、鼻腔、软腭、舌根、颏突，均0.5cm
+送检切缘：腮腺2,0.5cm
+左颈大块：9*6*4cm，为肌肉、脂肪、血管，灰黄。
+右颈大块：10*8*4cm，一侧见一腺体4*3*2cm，灰黄分叶，余为脂肪血管。
+左I区: 1只直径1cm。
+左II区: 2只直径0.5-1cm。
+左III区: 4只直径0.8-1.3cm。
+左IV区: 3只直径1.2-1.8cm。
+左V区: 1只直径1cm。
+右I区: 3只直径1-3.5cm。
+右II区: 3只直径0.8-2cm。
+右III区: 4只直径0.5-1cm。
+右IV区: 4只直径0.5-1.2cm。
+右V区: 2只直径0.5-0.8cm。
+"""
+Conclusion = """
+“左颊”黏膜鳞状细胞癌，高-中分化，DOI＞10mm
+送检切缘：“腮腺”阳性（+）、“前内、前外、上内、上外、颊、翼内肌、翼外肌、鼻底、鼻旁、鼻腔、软腭、舌根、颏突、腮腺2”均阴性（-）
+冰冻送检：“颏下淋巴结”1只内见鳞状细胞癌转移（+），侵犯至包膜外，“左IV区淋巴结”1只为软组织，伴出血
+“左颈大块”为软组织、“右颌下腺”轻度慢性炎
+送检淋巴结：“右I”1/3只有肿瘤转移（+），余及“左”“I”1只，“II”2只，“III”4只，“IV”3只，“V”1只，“右”“II”3只，“III”4只，“IV”4只，“V”2只均阴性（-）
+免疫组化结果NI21-695
+AE1/AE3+ CKH+ CK5/6+ EGFR部分+ Ki67部分+ CD31- S-100- P16-
+北院分子结果(NM2021-0316)：EGFR扩增探针 FISH（未见明显扩增（-））
+"""
+
+oral = Oral(Finding, Conclusion, verbose = False)
+
+
+##
+def get_color(text, entity_list, replaced_word, ImmunohistochemistryContent, MolecularResultsContent):
+    # print('replaced_word:', replaced_word)
+    # print(ImmunohistochemistryContent)
+    # print(MolecularResultsContent)
+    synonyms = []
+    for item in entity_list:
+        if item['tag'] == 'ANATOMY':
+            words_anatomy = item['words']
+            if item['words'] == 'I' or item['words'] == 'II' or item['words'] == 'III' or item['words'] == 'IV' or item[
+                'words'] == 'VI' or item['words'] == 'V' or item['words'] == '右' or item['words'] == '左':
+                words_anatomy = "“" + item['words'] + "”"
+            for i in re.finditer(
+                    words_anatomy.replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                synonyms.append(i.span())
+        if item['tag'] == 'OTHER':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                synonyms.append(i.span())
+    
+    negative = []
+    for i in re.finditer('无', text):
+        negative.append(i.span())
+    for i in re.finditer('未见', text):
+        negative.append(i.span())
+    for i in re.finditer('未发生', text):
+        negative.append(i.span())
+    
+    numeracal = []
+    for item in entity_list:
+        if item['tag'] == 'NUMBER':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                numeracal.append(i.span())
+        if item['tag'] == 'SIZE':
+            # if item['words']=='12*9*8cm':
+            #     print("^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
+            #     print(text)
+            #     for i in re.finditer(item['words'], text):
+            #         print(i)
+            #     print("^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
+            
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                numeracal.append(i.span())
+        if item['tag'] == 'DOI':
+            if replaced_word == '':
+                for i in re.finditer(
+                        item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'),
+                        text):
+                    numeracal.append(i.span())
+            else:
+                if item['words'] not in text:
+                    if replaced_word == '大于':
+                        doi_words = item['words'].replace(">", "大于")
+                    elif replaced_word == '小于':
+                        doi_words = item['words'].replace("<", "小于")
+                    elif replaced_word == '大于等于':
+                        doi_words = item['words'].replace("≥", "大于等于")
+                    elif replaced_word == '小于等于':
+                        doi_words = item['words'].replace("≤", "小于等于")
+                    elif replaced_word == '＞':
+                        doi_words = item['words'].replace(">", "＞")
+                    elif replaced_word == '小于':
+                        doi_words = item['words'].replace("<", "＜")
+                    for i in re.finditer(
+                            doi_words.replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'),
+                            text):
+                        numeracal.append(i.span())
+    
+    summary = []
+    for item in entity_list:
+        if item['tag'] == 'ENE':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                summary.append(i.span())
+        if item['tag'] == 'PN':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                summary.append(i.span())
+    
+    classification = []
+    for item in entity_list:
+        if item['tag'] == 'LEVEL':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                classification.append(i.span())
+    
+    other = []
+    for item in entity_list:
+        if item['tag'] == 'SQUAMOUS':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                other.append(i.span())
+        if item['tag'] == 'INVASION':
+            for i in re.finditer(
+                    item['words'].replace('*', '\*').replace('(', '\(').replace(')', '\)').replace('+', '\+'), text):
+                other.append(i.span())
+    if ImmunohistochemistryContent != '':
+        for i in re.split('。| |\n', ImmunohistochemistryContent):
+            # print(i)
+            if i == "" or i == "\n":
+                continue
+            for j in re.finditer(i, text):
+                # print(j)
+                other.append(j.span())
+    if MolecularResultsContent != '':
+        for i in re.split('。| |\n', MolecularResultsContent):
+            # print(i)
+            if i == "" or i == "\n":
+                continue
+            for j in re.finditer(i, text):
+                # print(j)
+                other.append(j.span())
+    
+    synonyms = list(set(synonyms))
+    negative = list(set(negative))
+    numeracal = list(set(numeracal))
+    summary = list(set(summary))
+    classification = list(set(classification))
+    other = list(set(other))
+    
+    return {
+        '医学术语解析': other,
+        '同义词判断': synonyms,
+        '识别否定修饰词及其修饰对象': negative,
+        '数值解析': numeracal,
+        '对可归纳总结的信息进行解析后归纳判断': summary,
+        '对定义明确的分类变量进行赋值': classification
+    }
+
+
+##
+if __name__ == '__main__':
+    
+    finding_list, conclusion_list, findind_replaced_word, conclusion_replaced_word, ImmunohistochemistryContent, MolecularResultsContent = oral.get_entity()
+    
+    for i in finding_list:
+        print(i)
+    r1 = get_color(Finding, finding_list, findind_replaced_word, ImmunohistochemistryContent, MolecularResultsContent)
+    print("\n医学术语解析:")
+    for i in r1['医学术语解析']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    print("\n同义词判断:")
+    for i in r1['同义词判断']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    print("\n识别否定修饰词及其修饰对象:")
+    for i in r1['识别否定修饰词及其修饰对象']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    print("\n数值解析:")
+    for i in r1['数值解析']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    print("\n对可归纳总结的信息进行解析后归纳判断:")
+    for i in r1['对可归纳总结的信息进行解析后归纳判断']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    print("\n对定义明确的分类变量进行赋值:")
+    for i in r1['对定义明确的分类变量进行赋值']:
+        print(Finding[i[0]: i[1]], i[0], i[1])
+    
+    print("\n*****************************************\n")
+    
+    for i in conclusion_list:
+        print(i)
+    r2 = get_color(Conclusion, conclusion_list, conclusion_replaced_word, ImmunohistochemistryContent,
+                   MolecularResultsContent)
+    print("\n医学术语解析:")
+    for i in r2['医学术语解析']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1])
+    print("\n同义词判断:")
+    for i in r2['同义词判断']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1], )
+    print("\n识别否定修饰词及其修饰对象:")
+    for i in r2['识别否定修饰词及其修饰对象']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1])
+    print("\n数值解析:")
+    for i in r2['数值解析']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1])
+    print("\n对可归纳总结的信息进行解析后归纳判断:")
+    for i in r2['对可归纳总结的信息进行解析后归纳判断']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1])
+    print("\n对定义明确的分类变量进行赋值:")
+    for i in r2['对定义明确的分类变量进行赋值']:
+        print(Conclusion[i[0]: i[1]], i[0], i[1])
+
+# ##
+# print(Conclusion[235:236])
+# print(Conclusion[179:180])
+# print(Conclusion[161:162])

model.py

@@ -17,12 +17,39 @@ class Oral:
         self._Conclusion = ''
         self._Finding = ''
         
+        self.inversed = False
+        
         if '送检淋巴结' in ImagingConclusion:
             self._Conclusion = ImagingConclusion
             self._Finding = ImagingFindings
         else:
             self._Conclusion = ImagingFindings
             self._Finding = ImagingConclusion
+            self.inversed = True
+        
+        self.conclusion_replaced_word = ''
+        self.findind_replaced_word = ''
+        if "大于" in self._Conclusion:
+            self.conclusion_replaced_word = "大于"
+        if "小于" in self._Conclusion:
+            self.conclusion_replaced_word = "小于"
+        if "大于等于" in self._Conclusion:
+            self.conclusion_replaced_word = "大于等于"
+        if "小于等于" in self._Conclusion:
+            self.conclusion_replaced_word = "小于等于"
+        if "＞" in self._Conclusion:
+            self.conclusion_replaced_word = "＞"
+        
+        if "大于" in self._Finding:
+            self.findind_replaced_word = "大于"
+        if "小于" in self._Finding:
+            self.findind_replaced_word = "小于"
+        if "大于等于" in self._Finding:
+            self.findind_replaced_word = "大于等于"
+        if "小于等于" in self._Finding:
+            self.findind_replaced_word = "小于等于"
+        if "＞" in self._Finding:
+            self.findind_replaced_word = "＞"
         
         self._Conclusion = self._Conclusion.strip('"').strip() \
             .replace("大于", ">").replace("小于", "<").replace("大于等于", "≥").replace("小于等于", "≤").replace("＞", ">").replace(
@@ -694,6 +721,21 @@ class Oral:
         for i in self._y_pre_o:
             print(i)
     
+    def get_entity(self):
+        finding_list = []
+        conclusion_list = []
+        if self.inversed == True:
+            for i in self._y_pre:
+                finding_list.append({'tag': i[0], 'words': i[1]})
+            for i in self._y_pre_o:
+                conclusion_list.append({'tag': i[0], 'words': i[1]})
+        else:
+            for i in self._y_pre_o:
+                finding_list.append({'tag': i[0], 'words': i[1]})
+            for i in self._y_pre:
+                conclusion_list.append({'tag': i[0], 'words': i[1]})
+        return finding_list, conclusion_list, self.findind_replaced_word, self.conclusion_replaced_word, self.ImmunohistochemistryContent, self.MolecularResultsContent
+    
     def print_list_item(self, l):
         for i in l:
             print(i)
@@ -735,21 +777,15 @@ class Oral:
 ##
 if __name__ == '__main__':
     Finding = """
-" 左颈大块：6*5*4cm，一侧见一腺体3*3*2cm，灰黄分叶，余为脂肪血管。
-左I区: 3只直径0.2-1.2cm。
-左II区: 3只直径0.5-1.2cm。
-左III区: 3只直径0.5-1cm。
-左IV区: 3只直径0.5-0.8cm。
-右I区：3只直径1-2cm。
-右II区: 3只直径1cm。
-右III区: 3只直径0.5-0.8cm。
-右IV区: 3只直径0.5-0.6cm。
-右颈淋巴：7*7*6cm，內见一腺体3*3*2cm，灰黄分叶，余为脂肪血管。"
+"1、一带黏膜组织，1.8*0.8*0.5cm。灰黄。（2全）。
+
+2、送检切缘：“前、后、左、右、底”均0.5cm。"
 """
     Conclusion = """
-"“左颌下腺”慢性涎腺炎
-“右颌下腺”慢性涎腺炎
-送检淋巴结：“左”“I区”1/3只、“II区”1/3只、“III区”1/3只（肿瘤位于软组织内）及“右”“I区”2/3只（其中1只肿瘤侵犯至包膜外）、“II区”2/3只（肿瘤侵犯至包膜外）有肿瘤转移（+），余及“左IV区”3只、“右”“III区”3只、“IV区”3只均阴性（-）"
+"“右口底”黏膜上皮中-重度异常增生及瘤样增生，癌变为鳞状细胞癌，高-中分化，DOI:小于5mm。
+送检切缘：“前、后、左、右、底”均阴性（-）。
+
+南院免疫组化结果(I2021-3047)：CKH（+），CK5/6（+），P16（-），Ki67（约30－40%+），CD31（-），S100（-），EGFR（+），P53（少量+）。"
 """
     
     oral = Oral(Finding, Conclusion)
@@ -758,4 +794,4 @@ if __name__ == '__main__':
     oral.print_y_pred_o()
     print("-----------------")
     oral.get_Info()
-    print(oral.get_json())
+    # print(oral.get_json())