class Document(object):
def __init__(self, templ_docx):
self._doc = DocxTemplate(templ_docx)
self._pic_to_render = {}
self._context = {}
self._chapter = {}
self._sequence = 0
def sequence(self):
self._sequence = self._sequence + 1
return self._sequence
def add_context(self, context={}):
self._context = context.copy()
def add_heading(self, title, level=1):
docx = self._doc.get_docx()
docx.add_heading(title, level)
def add_chapter(self, chapter, title=None, level=2, remove_file=True):
try:
docx = self._doc.get_docx()
if title is not None:
docx.add_heading(title, level)
id = "chapter" + str(self.sequence())
chapter.render()
docx.add_paragraph("{{p " + id + "}}")
self._chapter[id] = self._doc.new_subdoc(chapter.get_filename())
pic_to_add = chapter.get_pic_to_add()
if pic_to_add:
for pic in pic_to_add:
path = pic_to_add[pic]["path"]
width = pic_to_add[pic]["width"]
self._pic_to_render[pic] = InlineImage(self._doc,
path,
width=Mm(width))
finally:
if remove_file:
chapter.remove_file()
def inlineimage(self, image_file, image_width=147):
return InlineImage(self._doc, image_file, width=Mm(image_width))
def render(self):
if self._chapter or self._context:
self._context.update(self._chapter)
self._doc.render(self._context)
if self._pic_to_render:
self._doc.render(self._pic_to_render)
def save(self, filename):
self._doc.save(filename)
def excel2word(excel_path, word_path, output_path):
# 选择Excel 配置文件和Word 模板文件, 生成Word 报告
tpl = DocxTemplate(word_path)
wb = load_workbook(filename=excel_path)
context = {}
for sheetname in wb.sheetnames:
ws1 = wb[sheetname]
if sheetname == "条目配置":
context.update(get_item_config(ws1))
else:
document = tpl.new_subdoc()
context[f"table_{sheetname}"] = document
table = document.add_table(rows=ws1.max_row, cols=ws1.max_column)
table.style = "table"
for x in range(1, ws1.max_row + 1):
for y in range(1, ws1.max_column + 1):
c = ws1.cell(row=x, column=y, value=None)
if not type(c) == MergedCell:
table.rows[x - 1].cells[y - 1].text = str(c.value)
for cell in ws1.merged_cells:
# print(type(cell))
cells = list(cell.cells)
c_f = table.rows[cells[0][0] - 1].cells[cells[0][1] - 1]
c_l = table.rows[cells[-1][0] - 1].cells[cells[-1][1] - 1]
c_f.merge(c_l)
tpl.render(context)
tpl.save(output_path)
def get_page(self, id, doc):
context = {}
try:
id = int(id)
except:
return context.update({'error': 'id value is not int'})
page = Page.objects.filter(id=id)
if len(page) <= 0:
return context.update({'error': f'Page {id} not found'})
lpage = page[0]
if lpage.content_type.name.replace(' ', '') == 'meynstreampage':
lpage = getattr(lpage, lpage.content_type.name.replace(' ', '')).body
lblock = []
for block in lpage:
pass
if block.block_type in ('heading'):
lblock.append({'type': block.block_type, 'value': block.value})
elif block.block_type in ('paragraph'):
lblock.append({'type': block.block_type, 'value': self.html2sb(str(block.value), doc)})
elif block.block_type in ('warning'):
lblock.append({'type': block.block_type, 'value': self.html2sb(block.value.bound_blocks['warning'].value.source, doc)})
else:
logging.error(f"type : { block.block_type }")
subdoc_dir = os.path.join(settings.STATICFILES_DIRS[0], "template/other.docx")
doc = DocxTemplate(subdoc_dir)
subdoc = doc.new_subdoc().add_paragraph('un paragraphe')
lblock.append({'type': 'other', 'value': doc.build_xml({})})
context.update({'blocks': lblock})
return context
def main():
tmp_file = 'merge_columnout.csv'
preprocess_csv(input_csv, tmp_file)
tpl = DocxTemplate(template_docx)
sd = tpl.new_subdoc()
prev = None
with open(tmp_file, 'r') as f:
reader = csv.DictReader(f, delimiter=',')
for row in reader:
if prev is None or prev['Emplacement du jardin'] != row[
'Emplacement du jardin']:
_add_localisation_header(row['Emplacement du jardin'],
document=sd)
_create_new_entry_in_doc(row, document=sd)
prev = row
context = {
'mysubdoc': sd,
}
tpl.render(context)
tpl.save('output.docx')
def nccn():
"""
生成适应症癌种
:return:
"""
nccnpath = os.path.join(basepath, 'baseinfo', 'nccn.xlsx')
tplpath = os.path.join(basepath, 'template', 'blank.docx')
nccnxlsx = pd.read_excel(nccnpath, None)
for treadid, df in nccnxlsx.items():
df = df.fillna('NA')
tpl = DocxTemplate(tplpath)
sd = tpl.new_subdoc()
p = sd.add_paragraph('', style='02级标题')
sd.add_paragraph()
table = sd.add_table(rows=1, cols=3, style='1summary_common')
content = ['检测基因', '检测意义', '检测结果']
table.cell(0, 0).text = content[0]
table.cell(0, 1).text = content[1]
table.cell(0, 2).text = content[2]
nccndescribe = ''
for _, rows in df.iterrows():
gene = rows['检测基因']
if gene == 'info':
nccndescribe = rows['检测范围']
elif gene == '微卫星状态':
continue
elif gene == 'treatresult':
treatresult = rows['检测范围']
p.add_run('{}NCCN指南相关基因'.format(treatresult))
else:
rownum = len(table.rows)
common.add_tables_self(table, 1)
common.add_run_self(table.cell(rownum, 0).paragraphs[0], gene, font_size=8, alignment='left')
if rows['检测意义'] == 'NA':
table.cell(rownum, 1).merge(table.cell(rownum - 1, 1))
else:
common.add_run_self(table.cell(rownum, 1).paragraphs[0],rows['检测意义'],
font_size=8, alignment='other')
rlist = ['{{%p if nccn.{}.f %}}'.format(gene),
'{{{{ nccn.{0}.r }}}}'.format(gene),
'{{%p else %}}',
'{{{{ nccn.{0}.r }}}}'.format(gene),
'{{%p endif %}}']
for i in range(5):
if i > 0:
table.cell(rownum, 2).add_paragraph('')
if i == 1:
common.add_run_self(table.cell(rownum, 2).paragraphs[i], rlist[i], font_size=8,
font_color=(255, 99, 28), alignment='left')
else:
common.add_run_self(table.cell(rownum, 2).paragraphs[i], rlist[i], font_size=8,
alignment='left')
width = [2.74, 11, 4.0]
common.adjust_table_width(table, width)
sd.add_paragraph(nccndescribe, style='0星号段落')
word = os.path.join(basepath, 'template', '4medicaltip', 'nccn', f'{treadid}.docx')
context = {'context': sd}
tpl.render(context, autoescape=True)
tpl.save(word)
def space_group_subdoc(tpl_doc: DocxTemplate, cif: CifContainer) -> Subdoc:
"""
Generates a Subdoc subdocument with the xml code for a math element in MSWord.
"""
s = SpaceGroups()
try:
spgrxml = s.to_mathml(cif.space_group)
except KeyError:
spgrxml = '<math xmlns="http://www.w3.org/1998/Math/MathML">?</math>'
spgr_word = math_to_word(spgrxml)
# I have to create a subdocument in order to add the xml:
sd = tpl_doc.new_subdoc()
p: Paragraph = sd.add_paragraph()
p.alignment = WD_PARAGRAPH_ALIGNMENT.LEFT
p._element.append(spgr_word)
try:
p.add_run(' ({})'.format(cif.spgr_number))
except AttributeError:
pass
return sd
# -*- coding: utf-8 -*-
'''
Created : 2015-03-12
@author: Eric Lapouyade
'''
from docxtpl import DocxTemplate
from docx.shared import Inches
tpl=DocxTemplate('test_files/subdoc_tpl.docx')
sd = tpl.new_subdoc()
p = sd.add_paragraph('This is a sub-document inserted into a bigger one')
p = sd.add_paragraph('It has been ')
p.add_run('dynamically').style = 'dynamic'
p.add_run(' generated with python by using ')
p.add_run('python-docx').italic = True
p.add_run(' library')
sd.add_heading('Heading, level 1', level=1)
sd.add_paragraph('This is an Intense quote', style='IntenseQuote')
sd.add_paragraph('A picture :')
sd.add_picture('python_logo.png', width=Inches(1.25))
sd.add_paragraph('A Table :')
table = sd.add_table(rows=1, cols=3)
hdr_cells = table.rows[0].cells
hdr_cells[0].text = 'Qty'
hdr_cells[1].text = 'Id'
# -*- coding: utf-8 -*-
'''
Created : 2015-03-12
@author: Eric Lapouyade
'''
from docxtpl import DocxTemplate
tpl=DocxTemplate('test_files/subdoc_tpl.docx')
sd = tpl.new_subdoc()
p = sd.add_paragraph('This is a sub-document inserted into a bigger one')
p = sd.add_paragraph('It has been ')
p.add_run('dynamically').style = 'dynamic'
p.add_run(' generated with python by using ')
p.add_run('python-docx').italic = True
p.add_run(' library')
context = {
'mysubdoc' : sd,
}
tpl.render(context)
tpl.save('test_files/subdoc.docx')
# Run's color data
output_run.font.color.rgb = run.font.color.rgb
# Run's font data
output_run.style.name = run.style.name
# Paragraph's alignment data
output_para.paragraph_format.alignment = paragraph.paragraph_format.alignment
## make logic that if a line has capital letter each word or just one line no
## punctuation, make it bold?
## look at source code for docxcomposer - maybe i can use this to insert whole
## thing into
# %%
from docxtpl import DocxTemplate
from docx.shared import Inches
doc = DocxTemplate("templates/template.docx")
sd = doc.new_subdoc(docpath = 'articles/Article1.docx')
context = {
'mysubdoc': sd,
}
doc.render(context)
doc.save('generated_docs/subdoc_test.docx')
# %%
def genReport():
survey = request.args.get('survey')
company = request.args.get('company')
now = datetime.datetime.now()
curdate = now.strftime("%Y-%m-%d")
host, base, colection, dbuser, pwd = bl.mongoInit('users')
#file='C:\\toHDD\\toViggu\\surveyapp_python\\dataframe_1555184982.xlsx'
req = requests.get(
"http://localhost/backend/chartsAll?survey={}&company={}".format(
survey, company))
print(req.text)
file = req.text
r = requests.get(
"http://localhost/backend/getAllRadar?dataframe={}".format(file))
jsonres = r.json()
subscores = []
subscores.append(jsonres['Physical'][0])
subscores.append(jsonres['Organizational'][0])
subscores.append(jsonres['Technical'][0])
subscores.append(jsonres['Physical'][1])
subscores.append(jsonres['Organizational'][1])
subscores.append(jsonres['Technical'][1])
subscores.append(jsonres['Physical'][2])
subscores.append(jsonres['Organizational'][2])
subscores.append(jsonres['Technical'][2])
subscores.append(jsonres['Physical'][3])
subscores.append(jsonres['Organizational'][3])
subscores.append(jsonres['Technical'][3])
R0 = cl.genFullRadar(sectors, subsectors, subscores)
r = requests.get(
"http://localhost/backend/getAllRadarBySector?dataframe={}".format(
file))
jsonres = r.json()
R1_labels = jsonres[0]['labels']
R1_values = jsonres[0]['score']
R2_labels = jsonres[1]['labels']
R2_values = jsonres[1]['score']
R3_labels = jsonres[2]['labels']
R3_values = jsonres[2]['score']
R4_labels = jsonres[3]['labels']
R4_values = jsonres[3]['score']
R1 = cl.genRadar(R1_labels, R1_values, '#ff6666', 'Robustness')
R2 = cl.genRadar(R2_labels, R2_values, '#ffcc99', 'Redundancy')
R3 = cl.genRadar(R3_labels, R3_values, '#99ff99', 'Resourcefulness')
R4 = cl.genRadar(R4_labels, R4_values, '#66b3ff', 'Rapidity')
r = requests.get(
"http://localhost/backend/getAllRadarAllSectors?dataframe={}".format(
file))
jsonres = r.json()
labels = jsonres['category']
values = jsonres['scores']
print(values)
labels = pd.Series(labels)
values = pd.Series(values)
R5 = cl.barh(labels, values)
r = requests.get(
"http://localhost/backend/getAllRadar?dataframe={}".format(file))
jsonres = r.json()
phy = jsonres['Physical']
org = jsonres['Organizational']
tech = jsonres['Technical']
subsecs = ['Physical', 'Organizational', 'Technical']
bar1 = [phy[0], org[0], tech[0]]
bar2 = [phy[1], org[1], tech[1]]
bar3 = [phy[2], org[2], tech[2]]
bar4 = [phy[3], org[3], tech[3]]
R1_bar = cl.barRadar('R1', bar1, subsecs)
R2_bar = cl.barRadar('R2', bar2, subsecs)
R3_bar = cl.barRadar('R3', bar3, subsecs)
R4_bar = cl.barRadar('R4', bar4, subsecs)
lists = [R0, R1, R2, R3, R4, R5, R1_bar, R2_bar, R3_bar, R4_bar]
print(lists)
doc = DocxTemplate("sampleWord.docx")
s1 = doc.new_subdoc()
s1.add_picture(R1, width=Inches(7))
s2 = doc.new_subdoc()
s2.add_picture(R2, width=Inches(7))
s3 = doc.new_subdoc()
s3.add_picture(R3, width=Inches(7))
s4 = doc.new_subdoc()
s4.add_picture(R4, width=Inches(7))
s5 = doc.new_subdoc()
s5.add_picture(R0, width=Inches(7))
s6 = doc.new_subdoc()
s6.add_picture(R5, width=Inches(7))
s7 = doc.new_subdoc()
s7.add_picture(R1_bar, width=Inches(5))
s8 = doc.new_subdoc()
s8.add_picture(R2_bar, width=Inches(5))
s9 = doc.new_subdoc()
s9.add_picture(R3_bar, width=Inches(5))
s10 = doc.new_subdoc()
s10.add_picture(R4_bar, width=Inches(5))
req = requests.get(
"http://localhost/backend/surveysCount?survey={}&company={}".format(
survey, company))
count = req.text
context = {
'bar1': s7,
'bar2': s8,
'bar3': s9,
'bar4': s10,
'chart5': s6,
'radar1': s1,
'radar2': s2,
'radar3': s3,
'radar4': s4,
'complete': s5,
'company': company,
'survey': survey,
'date': curdate,
'number': count
}
doc.render(context)
filename = "Survey_Metrics_{}.docx".format(bl.getTimeStamp())
doc.save(filename)
outputFile = bl.convertToPDF(filename)
bl.sendReport(survey, company, outputFile)
return "Sent Report"
# -*- coding: utf-8 -*-
'''
Created : 2021-07-30
@author: Eric Lapouyade
'''
from docxtpl import DocxTemplate
tpl = DocxTemplate('templates/merge_docx_master_tpl.docx')
sd = tpl.new_subdoc('templates/merge_docx_subdoc.docx')
context = {
'mysubdoc': sd,
}
tpl.render(context)
tpl.save('output/merge_docx.docx')
class doc(object):
def __init__(self):
base_url = getDir() + '/user/user_template/' #初始化生成一个doc对象
asset_url = base_url + 'demo.docx'
self.tpl = DocxTemplate(asset_url)
self.webvul = self.tpl.new_subdoc() #web应用漏洞
self.appvul = self.tpl.new_subdoc() #应用程序漏洞
self.devicevul = self.tpl.new_subdoc() #网络设备漏洞
self.sysvul = self.tpl.new_subdoc() #操作系统应用漏洞
self.time = self.tpl.new_subdoc()
self.number = 0
def add_title(self, title, type , level=3):
doc = self.check_type(type)
run = doc.add_heading('', level=level).add_run(title)
run.font.name = "宋体"
run.font.size = Pt(14)
r = run.element
r.rPr.rFonts.set(qn('w:eastAsia'), u'宋体')
def add_table(self,jsons, type=1):
'''
在doc中添加表格
:param json:
type:1为web漏洞2为应用程序漏洞,3为网络设备漏洞4为系统漏洞
:return:
'''
#获取要写入的subdoc节点
doc = self.check_type(type)
for json in jsons:
# j控制json字典下标
#print(json)
j = 0
title = json['title'] #生成标题
self.number += 1
self.add_title(title,type=type)
table = doc.add_table(rows=len(json)-1, cols=2, style="Style1")#新建一个表格
table.autofit = False
for key, value in json.items():
if j == 0:
j +=1
else:
table.columns[0].width = Cm(3)
table.columns[1].width = Cm(12)
table.cell(j - 1, 0).width = Cm(3) #设置单元格宽度
table.cell(j - 1, 1).width = Cm(12)
#table.alignment=WD_TABLE_ALIGNMENT.RIGHT 设置对齐方式
keyCell = table.cell(j-1, 0) #表格赋值
valueCell = table.cell(j-1, 1)
#设置key单元格字体与字体大小
key_paragraph = keyCell.paragraphs[0]
#keyRun = keyCell.paragraphs[0].add_run(key)
keyRun = key_paragraph.add_run(key)
keyRun.font.name = u'微软雅黑' # 设置字体
keyRun._element.rPr.rFonts.set(qn('w:eastAsia'), u'微软雅黑')
keyRun.font.size = Pt(10.5) # 设置字号为五号
key_paragraph.paragraph_format.line_spacing = WD_LINE_SPACING.ONE_POINT_FIVE#设置1.5倍行间距
key_paragraph.paragraph_format.alignment = WD_PARAGRAPH_ALIGNMENT.RIGHT #设置水平对齐方式右对齐
keyCell.vertical_alignment = WD_CELL_VERTICAL_ALIGNMENT.CENTER
#设置value单元格字体与字体大小
val_paragraph = valueCell.paragraphs[0]
#valueRun = valueCell.paragraphs[0].add_run(value) # 填入的内容
valueRun = val_paragraph.add_run(value)
valueRun.font.name = u'微软雅黑' # 设置字体
valueRun.font.size = Pt(10.5) # 设置字号为五号
valueRun._element.rPr.rFonts.set(qn('w:eastAsia'), u'微软雅黑')
val_paragraph.paragraph_format.line_spacing_rule = WD_LINE_SPACING.ONE_POINT_FIVE#设置1.5倍行间距
val_paragraph.paragraph_format.alignment = WD_PARAGRAPH_ALIGNMENT.LEFT#设置水平对齐方式左对齐
valueCell.vertical_alignment = WD_CELL_VERTICAL_ALIGNMENT.CENTER
#keyCell.text = key
#valueCell.text = value
#print(key,value)
j = j+1
#赋值给初始话的subdoc值
if type==1:
self.webvul=doc
elif type==2:
self.appvul= doc
elif type==3:
self.devicevul = doc
else:
self.sysvul = doc
#保存docx文档
def save_doc(self,current_time, start_time):
#添加doc编辑时间
filename = "上海驭胜信息安全通告（%s至%s).docx" % (str(start_time),str(current_time))
content = {'subdoc': self.webvul,
'appdoc':self.appvul,
'devicedoc': self.devicevul,
'sysdoc': self.sysvul,
'time': current_time ,
'start_time': start_time,
'end_time': current_time}
self.tpl.render(content)
self.tpl.save(filename)
print("file %s success to save!" % filename)
def check_type(self,num):
if num==1:
return self.webvul
elif num ==2:
return self.appvul
elif num ==3:
return self.devicevul
else:
return self.sysvul
def add_hyperlink(self,paragraph, text, url):
# This gets access to the document.xml.rels file and gets a new relation id value
part = paragraph.part
r_id = part.relate_to(url, docx.opc.constants.RELATIONSHIP_TYPE.HYPERLINK, is_external=True)
# Create the w:hyperlink tag and add needed values
hyperlink = docx.oxml.shared.OxmlElement('w:hyperlink')
hyperlink.set(docx.oxml.shared.qn('r:id'), r_id, )
# Create a w:r element and a new w:rPr element
new_run = docx.oxml.shared.OxmlElement('w:r')
rPr = docx.oxml.shared.OxmlElement('w:rPr')
# Join all the xml elements together add add the required text to the w:r element
new_run.append(rPr)
new_run.text = text
hyperlink.append(new_run)
# Create a new Run object and add the hyperlink into it
r = paragraph.add_run ()
r.font.name = u'微软雅黑' # 设置字体
r.font.size = Pt(10.5) # 设置字号为五号
r._element.rPr.rFonts.set(qn('w:eastAsia'), u'微软雅黑')
r._r.append (hyperlink)
# A workaround for the lack of a hyperlink style (doesn't go purple after using the link)
# Delete this if using a template that has the hyperlink style in it
r.font.color.theme_color = MSO_THEME_COLOR_INDEX.HYPERLINK
r.font.underline = True
return hyperlink
from docxtpl import DocxTemplate
doc = DocxTemplate("黄浦投资意见书.docx")
sd = doc.new_subdoc('sub.docx')
context = {
't1': 'tttttttttttttt1',
't2': 'tttttttttttttt2',
'sub': sd,
}
doc.render(context)
doc.save("generated_doc.docx")
def reportBuild(featurePath, wmPath, gmPath, csfPath, hippoPath,
originImagePath, tempDir):
Volume = ""
SurfaceArea = ""
AreaVolume = ""
Uniformity = ""
Energy = ""
Entropy = ""
Variance = ""
wmVolume = ""
gmVolume = ""
csfVolume = ""
totalVolume = ""
wmVper = ""
gmVper = ""
csfVper = ""
leftVolume = ""
rightVolume = ""
if (featurePath is not None):
with open(featurePath, 'r') as f:
featureData = csv.DictReader(f)
featureDict = [row for row in featureData][0]
Volume = float(featureDict["original_shape_VoxelVolume"])
SurfaceArea = round(float(featureDict['original_shape_SurfaceArea']),
3)
AreaVolume = round(
float(featureDict["original_shape_SurfaceVolumeRatio"]), 3)
Median = round(float(featureDict['original_firstorder_Median']), 3)
Mean = round(float(featureDict['original_firstorder_Mean']), 3)
SurfaceAreaMark = compare(SurfaceArea, 3728.80, 4276.30)
AreaVolumeMark = compare(AreaVolume, 0.610, 0.689)
MedianMark = compare(Median, 1.58, 1.75)
MeanMark = compare(Mean, 1.59, 1.75)
#Uniformity = featureDict["original_firstorder_Uniformity"]
#Energy = featureDict["original_firstorder_Energy"]
#Entropy = featureDict["original_firstorder_Entropy"]
#Variance = featureDict["original_firstorder_Variance"]
hippoVolumeImagePath = os.path.join(tempDir, "hippoVolume.png")
drawDis(u=stdDistribution["NChippoVolumeMean"],
subject=Volume,
xlabel="海马体积 / mm3",
sig=stdDistribution["NChippoVolumeStd"],
u2=stdDistribution["ADhippoVolumeMean"],
sig2=stdDistribution["ADhippoVolumeStd"],
savePath=hippoVolumeImagePath)
if (wmPath is not None):
wmImage = nib.load(wmPath)
gmImage = nib.load(gmPath)
csfImage = nib.load(csfPath)
wmVolume = np.sum(wmImage.get_fdata().flatten())
wmVolume = round(wmVolume, 2)
gmVolume = np.sum(gmImage.get_fdata().flatten())
gmVolume = round(gmVolume, 2)
csfVolume = np.sum(csfImage.get_fdata().flatten())
csfVolume = round(csfVolume, 2)
totalVolume = wmVolume + gmVolume + csfVolume
totalVolume = round(totalVolume, 2)
wmVperData = float(int(wmVolume / totalVolume * 1000)) / 10
gmVperData = float(int(gmVolume / totalVolume * 1000)) / 10
csfVperData = float(int(csfVolume / totalVolume * 1000)) / 10
wmVper = str(wmVperData) + "%"
gmVper = str(gmVperData) + "%"
csfVper = str(csfVperData) + "%"
brainDignose = ""
if (wmVperData < reference["wmPer"][0]):
brainDignose += "白质体积占比减少；"
elif (wmVperData > reference["wmPer"][1]):
brainDignose += "白质体积占比增加；"
if (gmVperData < reference["gmPer"][0]):
brainDignose += "灰质体积占比减少；"
elif (gmVperData > reference["gmPer"][1]):
brainDignose += "灰质体积占比增加；"
if (csfVperData < reference["csfPer"][0]):
brainDignose += "脑脊液体积占比减少；"
elif (wmVperData > reference["csfPer"][1]):
brainDignose += "脑脊液体积占比增加；"
if (brainDignose == ""):
brainDignose += "未见明显异常"
VolumeDistributionImagePath = os.path.join(tempDir, "volume.png")
drawDis(u=stdDistribution["NCgmMeanPer"],
subject=gmVperData,
xlabel="灰质体积占比 / % ",
sig=stdDistribution["NCgmStdPer"],
u2=stdDistribution['ADgmMeanPer'],
sig2=stdDistribution['ADgmStdPer'],
savePath=VolumeDistributionImagePath)
hippoDignose = ""
if (hippoPath is not None):
hippoImage = nib.load(hippoPath)
leftHippo = hippoImage.get_fdata()[0:91, :, :]
rightHippo = hippoImage.get_fdata()[91:, :, :]
leftVolume = np.sum(leftHippo.flatten())
rightVolume = np.sum(rightHippo.flatten())
leftVolumeMark = ""
if (leftVolume < reference["leftVolume"][0]):
leftVolumeMark = "↓"
hippoDignose += "左侧海马体积减少；"
elif (leftVolume > reference["leftVolume"][1]):
leftVolumeMark = "↑"
hippoDignose += "左侧海马体积增加；"
rightVolumeMark = ""
if (rightVolume < reference["rightVolume"][0]):
rightVolumeMark = "↓"
hippoDignose += "右侧海马体积减少；"
elif (rightVolume > reference["rightVolume"][1]):
rightVolumeMark = "↑"
hippoDignose += "右侧海马体积增加；"
if (hippoDignose == ""):
hippoDignose += "未见明显异常"
hippoImagePngPath = os.path.join(tempDir, "hippoimage.png")
drawRoi(originImagePath, hippoPath, hippoImagePngPath)
path = os.path.dirname(os.path.realpath(__file__))
doc = DocxTemplate(os.path.join(path, "./Report.docx"))
sd = doc.new_subdoc()
#sd.add_paragraph(' :')
rows = 30
cols = 4
table = sd.add_table(rows=rows, cols=cols, style="mystyle")
#
# # header
cells = table.rows[0].cells
cells[0].text = "指标"
cells[1].text = "值"
cells[2].text = "参考范围"
cells[3].text = "备注"
referencePath = os.path.join(path, "feature.csv")
with open(referencePath, 'r') as f:
refData = csv.DictReader(f)
refDicts = [row for row in refData]
i = 1
for ref in refDicts:
if (i > 29):
break
featureName = ref['feature']
featureValue = float(featureDict[featureName])
refDataF = str(round(
float(ref['NC-mean']) - float(ref['NC-std']), 2)) + "~" + str(
round(float(ref['NC-mean']) + float(ref['NC-std']), 2))
remark = ""
if (featureValue < float(ref['NC-mean']) - float(ref['NC-std'])):
remark = "↓"
elif (featureValue > float(ref['NC-mean']) + float(ref['NC-std'])):
remark = "↑"
table.cell(i, 0).text = featureName
table.cell(i, 1).text = str(round(featureValue, 2))
table.cell(i, 2).text = str(refDataF)
table.cell(i, 3).text = remark
i += 1
context = {
'SubjectName':
"Test Subject",
"VolumeDistributionImage":
InlineImage(doc, VolumeDistributionImagePath, width=Mm(130)),
"HippoImage":
InlineImage(doc, hippoImagePngPath, width=Mm(130)),
"HippoDistributionImage":
InlineImage(doc, hippoVolumeImagePath, width=Mm(130)),
"Volume":
Volume,
"SurfaceArea":
SurfaceArea,
"AreaVolume":
AreaVolume,
"Median":
Median,
"Mean":
Mean,
"wmVolume":
wmVolume,
"gmVolume":
gmVolume,
"csfVolume":
csfVolume,
"totalVolume":
totalVolume,
"wmVper":
wmVper,
"gmVper":
gmVper,
"csfVper":
csfVper,
"leftVolume":
leftVolume,
"rightVolume":
rightVolume,
'mytable':
sd,
"SurfaceAreaMark":
SurfaceAreaMark,
"AreaVolumeMark":
AreaVolumeMark,
"MedianMark":
MedianMark,
"MeanMark":
MeanMark,
"leftVolumeMark":
leftVolumeMark,
"rightVolumeMark":
rightVolumeMark,
"brainDignose":
brainDignose,
"hippoDignose":
hippoDignose,
"rightVolumeRef":
str(reference["rightVolume"][0]) + "~" +
str(reference["rightVolume"][1]),
"leftVolumeRef":
str(reference["leftVolume"][0]) + "~" +
str(reference["leftVolume"][1]),
}
doc.render(context)
doc.save(
os.path.realpath(
os.path.join(tempDir,
os.path.basename(originImagePath) + ".docx")))
def main():
### MARK1 抓取命令行参数
parser = argparse.ArgumentParser(
prog='PGS_report',
description=
'Save PGS project\'s graph (.png) file to a (.docx) word file and sex info file to an excel (.xlsx) file and write a report based on word template to a (.docx) file. '
)
parser.add_argument(
'--project_type',
action="store",
required=False,
default="PGS",
choices=["PGS", "ChromInst", "ONCPGD", "ONPGS", "CPGD", "IBPGS"],
help="The Project type. [default=PGS]")
parser.add_argument('--project_dir',
action="store",
required=True,
help='The project output directory')
parser.add_argument('--bin_size',
action="store",
required=True,
help='The bin size, like 1000K. ')
parser.add_argument(
'--cnv_file',
action="store",
required=True,
help=
'The call cnv file created by pipeline. It is used to create the sex info excel file and PGS test results are extracted from it.'
)
parser.add_argument('--patient_info',
action="store",
required=True,
help='The patient info txt file')
parser.add_argument(
'--out_dir',
action="store",
required=True,
help='The output graph/info/report files\'s directory ')
parser.add_argument('--data_sts',
action="store",
required=True,
help="data.sts file")
args = parser.parse_args()
project_type = args.project_type
project_dir = os.path.abspath(args.project_dir)
bin_size = args.bin_size
cnv_file = os.path.abspath(args.cnv_file)
patient_info = os.path.abspath(args.patient_info)
out_dir = os.path.abspath(args.out_dir)
data_sts = os.path.abspath(args.data_sts)
### MARK2 解析参数文件，转化为变量
logger = create_logging('PGS report logger')
## MARK2.1 解析送检单 patient_info
dict_patient_info, dict_sample_info, sample_barcodes = parse_patient_info(
patient_info)
logger.info("DONE:parse patient info")
# MARK2.1.1 将缺失值“单击此处输入文字”替换为空字符
for (k, v) in dict_patient_info.items():
if v in MISSING_VALUES:
dict_patient_info[k] = ''
logger.info("DONE:clean patient info")
# 信息抓取补充
######read qc_discription.txt
dict_qc = {}
fh_sts = open(data_sts)
for line in fh_sts.readlines():
if line.split():
line = line.rstrip()
list_sts = line.split("\t")
dict_qc[list_sts[0]] = list_sts[10]
logger.info("DONE:parse data.sts")
## MARK2.2 解析结果 cnv_file
result_barcodes, dict_result, dict_result_gender = parse_cnv_file(
cnv_file, dict_qc)
logger.info("DONE:parse cnv file")
## MARK2.3 解析cnv图
dict_red_blue_png_no_XY = parse_graph(project_dir, 'graph',
'with_chrID_no_XY', result_barcodes,
bin_size)
dict_red_blue_png_XY = parse_graph(project_dir, 'graph',
'with_chrID_with_XY', result_barcodes,
bin_size)
dict_colorful_png_XY = parse_graph(project_dir, 'graph1',
'with_chrID_with_XY', result_barcodes,
bin_size)
logger.info("DONE:parse png graph")
### MARK3 根据需求，生成内部参量
## MARK 2018/3/1补充，由送检barcode和结果barcode，生成一个新的用于出结果的barcode
report_barcodes = gen_report_barcodes(sample_barcodes, result_barcodes)
## MARK3.1 抓取 项目名，医院名，女方姓名，是否要logo
# sample_sheet_ID 项目名
sample_sheet_ID = dict_patient_info["ProjectID"]
if sample_sheet_ID in MISSING_VALUES:
logger.error("Project ID is missing!")
exit(1)
# hospital_ID 医院名
array_sample_sheet_ID = sample_sheet_ID.split('_')
hospital_ID = array_sample_sheet_ID[3]
# woman_name 女方姓名
woman_name = dict_patient_info['WomanName']
if 'Control' in sample_sheet_ID or 'control' in sample_sheet_ID:
woman_name = 'Control'
# if_logo 是否要logo
if_logo = dict_patient_info['Template']
## MARK3.2 完整的输出名
out_name = "Project_" + sample_sheet_ID + u"（" + woman_name + u"）"
if woman_name == '':
out_name = "Project_" + sample_sheet_ID
### MARK4 结果展示
#######################
## MARK4.1 生成CNV全图
# CNV全图名
out_graph = out_dir + '/' + out_name + u"CNV全图.docx"
document = Document()
for barcode in report_barcodes:
png_fullpath = dict_colorful_png_XY[barcode]
if os.path.exists(png_fullpath):
document.add_picture(png_fullpath, width=Inches(6.35))
else:
log = "save graph file : " + png_fullpath + " does not exist!"
logger.warning(log)
document.save(out_graph)
logger.info("DONE:save graph file")
############################################################
## MARK4.2 生成性别信息表
# 性别信息名
out_info = out_dir + '/' + out_name + "info.xlsx"
wb = Workbook()
ws = wb.active
ws.title = "info"
excel_row = 1
for barcode in report_barcodes:
ws.cell(row=excel_row, column=1, value=barcode)
ws.cell(row=excel_row,
column=2,
value=dict_sample_info.get(barcode, barcode))
ws.cell(row=excel_row, column=3, value=dict_result_gender[barcode])
excel_row += 1
ws = adjustColumnWidth(ws)
wb.save(out_info)
logger.info("DONE:save sex info xlsx file")
####################
## MARK4.3 生成报告
## MARK 报告名
project_type_name = ''
if project_type == 'ONCPGD' or project_type == 'ONPGS':
project_type_name = "24h-胚胎染色体拷贝数检测报告单"
elif project_type == 'CPGD':
project_type_name = "MALBAC-PGD™ 染色体病胚胎植入前遗传学诊断报告单"
elif project_type == 'PGS' or project_type == 'IBPGS':
project_type_name = "胚胎植入前遗传学筛查（PGS）检测报告单"
else:
project_type_name = "ChromInst 9h-胚胎染色体拷贝数检测报告单"
out_report = out_dir + '/' + out_name + project_type_name + ".docx"
## MARK 报告模板
if project_type == 'ONCPGD' or project_type == 'ONPGS':
report_temp = ONCPGD_REPORT_TEMPLATE
elif project_type == 'CPGD':
report_temp = CPGD_REPORT_TEMPLATE
else:
if if_logo == "Yes" or if_logo == "yes":
report_temp = PGS_REPORT_TEMPLATE
else:
report_temp = PGS_REPORT_TEMPLATE_WITHOUT_LOGO
# MARK4.3.1 定制化
# 某些医院要求不写医院名
if hospital_ID in HOSPITAL_ID_WITHOUT_HOSPITAL_NAME:
dict_patient_info["SubmissionOrganization"] = ''
# ONCPGD活检日期填到送检日期位置
if project_type == 'ONCPGD' or project_type == 'ONPGS':
dict_patient_info["SubmissionDate"] = dict_patient_info["BiopsyDate"]
### MARK4.3.4 取模版，贴报告
shutil.copyfile(report_temp, out_report)
ReportTML = DocxTemplate(out_report)
## 报_送检信息
# 获取报告日期
now = datetime.datetime.now()
month = now.month
day = now.day
if month < 10:
month = '0' + str(month)
if day < 10:
day = '0' + str(day)
report_date = u"{}年{}月{}日".format(now.year, month, day)
context = dict_patient_info
context['ReportDate'] = report_date
## 报_核型
result = []
for barcode in report_barcodes:
tmp_dict = {
'sample_id': dict_sample_info.get(barcode, barcode),
'sample_barcode': barcode,
'test_result': dict_result[barcode]
}
result.append(tmp_dict)
context['result'] = result
## 报_图片
# 确定报告中用的红蓝图
dict_report_png = {}
report_png = ''
for barcode in result_barcodes:
red_blue_no_XY = dict_red_blue_png_no_XY[barcode]
red_blue_XY = dict_red_blue_png_XY[barcode]
if dict_result_gender[barcode] == "XX" or dict_result_gender[
barcode] == "XY":
report_png = red_blue_no_XY
elif dict_result[barcode] == "N/A":
report_png = red_blue_no_XY
else:
report_png = red_blue_XY
dict_report_png[barcode] = report_png
subdoc_picture = ReportTML.new_subdoc()
for barcode in report_barcodes:
doc_png = dict_report_png[barcode]
if os.path.exists(doc_png):
subdoc_picture.add_picture(doc_png, width=Inches(6.1))
else:
log = "save report file: " + doc_png + " does not exist!"
logger.warning(log)
context['subdoc_picture'] = subdoc_picture
# 写入，报告完成
ReportTML.render(context)
ReportTML.save(out_report)
logger.info("DONE:save report file")
