def _default_folder(
self
): #/Users/thomasaref/Dropbox (Clan Aref)/Current stuff/Logbook/TA210715A53_cooldown022915
return Folder(
base_dir=
"/Users/thomasaref/Dropbox (Clan Aref)/Current stuff/Logbook/TA210715A53_cooldown022915",
quality="",
main_dir="Data_0221")
def _default_folder(self):
return Folder(show_details=False, show_simple=False)
def _default_folder(self):
return Folder(base_dir="/Users/thomasaref/Dropbox/Current stuff/Logbook/TA210715A88_cooldown210216/tex_source_files/TA88_processed")
class TEX(Operative):
"""A laTeX/python report maker. source tex and images are included from the source folder. tex and python are written out to the save_file and save_code.
various subfunctions give easy access to including analysis written in python in a laTeX report"""
base_name = "tex"
#initial_size=(800,800)
folder = Folder(
base_dir="/Users/thomasaref/Dropbox/Current stuff/test_data")
source_folder = Folder(
base_dir="/Users/thomasaref/Dropbox/Current stuff/test_data",
main_dir="",
quality="")
read_file = Typed(Read_TXT)
save_file = Typed(Save_TXT)
save_code = Typed(Save_TXT)
plots_to_save = List()
def __init__(self, **kwargs):
source_path = kwargs.pop("source_path", None)
starter = kwargs.pop("starter", "TEX_start")
stopper = kwargs.pop("stopper", "TEX_end")
super(TEX, self).__init__(**kwargs)
self.interact.file_reader = File_Parser(starter=starter,
stopper=stopper)
if source_path is not None:
self.read_file.file_path = source_path
if self.read_file.folder.main_dir != "":
self.read_source()
def _default_read_file(self):
return Read_TXT(folder=self.source_folder, file_suffix=".tex")
def _default_save_file(self):
return Save_TXT(folder=self.folder,
file_name="report",
file_suffix=".tex",
fixed_mode=True)
def _default_save_code(self):
return Save_TXT(folder=self.save_file.folder,
file_name=self.save_file.file_name + "_code",
file_suffix=".py",
fixed_mode=True)
source_dict = Typed(OrderedDict, ())
tex_list = List()
output_tex = Unicode()
user_name = Unicode("Thomas Aref")
tex_title = Unicode("Sample TA210715A46 in Speedy 3-10-15 cooldown")
department = Unicode(
r"Department of Microtechnology and Nanoscience (MC2), Chalmers University of Technology, SE-412 96 G\"oteborg, Sweden"
)
tex_start = List()
tex_end = List()
fig_width = Float(0.49)
caption = Unicode()
locals_dict = Dict()
def _default_tex_start(self):
"""This list specifies the starting preamble for the laTeX document and should contain \begin{document} as well as any packages desired"""
return [
r"\documentclass[12pt,a4paper]{article}",
r"\usepackage[top=1 in, bottom=1 in, left=1 in, right=1 in]{geometry}",
r"\usepackage{amsfonts,amssymb,amsmath}", r"\usepackage{graphicx}",
r"\usepackage{hyperref}", r"\usepackage{color}",
r"\usepackage{placeins}", r"%\usepackage{tikz}",
r"%\usepackage[siunitx]{circuitikz}", r"%\usepackage{cite}",
r"\usepackage{caption}", r"\usepackage{subcaption}",
r"\usepackage{rotating}", r"\usepackage{paralist}",
r"\usepackage{cprotect}", r"",
r"\definecolor{red}{rgb}{1, 0, 0} %used for making comments in red color text",
r"\definecolor{green}{rgb}{0, 0.7, 0}",
r"\definecolor{blue}{rgb}{0, 0, 1}",
r"\newcommand{\mc}{\textcolor{red}} %used for making comments in red color text remove before submit",
r"\newcommand{\mg}{\textcolor{green}} %used for making comments in red color text remove before submit",
r"\newcommand{\mb}{\textcolor{blue}} %used for making comments in red color text remove before submit",
r"\newcommand{\comment}[1]{} %used for commenting out blocks of text remove before submit",
r"\newcommand{\pyb}[1]{} % do nothing command for marking for python extraction",
r"\newcommand{\pye}{} % do nothing command for python extraction end",
r"", r"", r"\begin{document}", r"\author{{{0}}}".format(
self.user_name), r"%\inst{{3}} {{{0}}}".format(
self.department), r"\title{{{0}}}".format(
self.tex_title), r"\maketitle", r"\noindent"
]
def _default_tex_end(self):
"""this list specifies the ending postamble of the latex document. could include bibtex for example"""
return [r"\end{document}"]
def _observe_output_tex(self, change):
"""syncs changes in the output tex of the GUI to tex_list"""
self.tex_list = self.output_tex.split("\n")
def simulate_tex(self):
"""simulates the python code producing the output texlist"""
self.interact.exec_code()
def restore_source(self):
"""process the source_dict to make the tex list just show the \pyb/\pye entries in source_dict"""
self.tex_list = []
for key in self.source_dict:
self.tex_list.extend(self.source_dict[key])
self.output_tex = "\n".join(self.tex_list)
def process_source(self):
"""process the tex_list to produce the source_dict and then calls restore_source"""
self.source_dict = OrderedDict()
for n, line in enumerate(self.tex_list):
line = line.strip()
if line.startswith("\pyb"):
index = n
key = line.split("\pyb")[1].split("{")[1].split("}")[0].strip()
elif line.startswith("\pye"):
self.source_dict[key] = [
item for item in self.tex_list[index:n + 1]
]
self.source_dict[key].append("")
self.restore_source()
def read_source(self, file_path=None):
"""reads a tex file in from read_file and processes it"""
if file_path is not None:
self.read_file.file_path = file_path
self.tex_list = self.read_file.read()
self.process_source()
def compile_tex(self):
"""compiles the tex file saved as save_file"""
compile_tex(self.save_file.folder.dir_path, self.save_file.file_name)
def open_pdf(self):
"""opens the pdf with the same no suffix name as save_file"""
call(["open", self.save_file.nosuffix_file_path + ".pdf"])
def make_tex_file(self):
"""saves the tex file using the latest version of input_code and tex_list if the GUI is active.
also saves a copy of the input_code with the preamble and postamble reattached"""
self.plots_to_save = []
if QtApplication.instance() is not None:
self.process_source()
self.simulate_tex()
self.save_file.save(self.tex_list, write_mode="w", flush_buffer=True)
for pl in self.plots_to_save:
pl.savefig(dir_path=self.folder.dir_path + self.folder.divider,
fig_name=pl.fig_name)
self.interact.get_member("code_str").reset(self)
self.save_code.save(self.interact.code_str,
write_mode="w",
flush_buffer=True)
def make_and_show(self):
"""makes the tex file, compiles the tex file and opens the pdf"""
self.make_tex_file()
self.compile_tex()
#self.open_pdf()
def TEX_start(self, clear=True, refresh=True):
"""starts the tex file and serves as a start marker for self.file_reader"""
if clear:
self.tex_list = []
if refresh:
self.tex_start = self._default_tex_start()
self.extend(self.tex_start)
#self.interact.make_input_code()
def TEX_end(self):
"""ends the tex file and serves as a stop marker for self.file_reader"""
self.extend(self.tex_end)
self.output_tex = "\n".join(self.tex_list)
def ext(self, block_name):
"""inserts the item corresponding to key block name from source_dict"""
self.extend(self.source_dict[block_name])
def add(self, inline):
"""adds tex given by string inline"""
self.tex_list.append(inline)
def extend(self, inlist):
"""extends texlist with inlist"""
self.tex_list.extend(inlist)
def make_table(self, table_values, table_format=None):
make_table(self.tex_list, table_values, table_format)
def include_figure(graph_gen,
tex,
fig_name,
caption="",
label="",
**kwargs):
"""uses the passed function graph_gen and kwargs to generate a figure and save it to the given file path"""
pl = graph_gen(**kwargs)
file_name = graph_gen.func_code.co_filename.split("Documents")[1]
caption = "{0} Analysis: \\verb;{1};".format(caption, file_name)
tex.append(r"\begin{figure}[ht!]")
tex.append(r"\centering")
tex.append(
"\\includegraphics[width=\\textwidth]{{{}}}".format(fig_name))
tex.append("\\cprotect\\caption{{{}}}".format(caption))
tex.append("\\label{{{}}}".format(label))
tex.append(r"\end{figure}")
#savefig(dir_path+fig_name, bbox_inches='tight')
#close()
def add_mult_image(self, fig_name, caption="", label=""):
"""inserts th image specified by dir_path and fig_name into the list tex"""
relative_path = relpath(
self.source_folder.dir_path,
self.save_file.folder.dir_path) + self.source_folder.divider
self.tex_list.extend([
"\\begin{{subfigure}}[b]{{{}\\textwidth}}".format(self.fig_width),
"\\includegraphics[width=\\textwidth]{{{}}}".format(relative_path +
fig_name),
#"\\cprotect\\caption{{{}}}".format(caption),
"\\label{{{}}}".format(label),
r"\end{subfigure}"
])
self.caption = caption
#include_image(self.tex_list, relative_path, fig_name, caption, label)
def add_mult_fig(self, graph_gen, fig_name, **kwargs):
"""adds a graph to a multi figure using the function graph_gen and given kwargs"""
if fig_name not in [p.fig_name for p in self.plots_to_save]:
pl = graph_gen(**kwargs)
pl.fig_name = fig_name
self.plots_to_save.append(pl)
file_name = graph_gen.func_code.co_filename.split("Documents")[1]
#savefig(dir_path+fig_name, bbox_inches='tight')
#close()
self.tex_list.extend([
"\\begin{{subfigure}}[b]{{{}\\textwidth}}".format(self.fig_width),
"\\includegraphics[width=\\textwidth]{{{}}}".format(fig_name),
#"\\cprotect\\caption{{{}}}".format(caption),
r"\end{subfigure}"
])
self.caption = "Analysis: \\verb;{0};".format(file_name)
def mult_fig_start(self):
mult_fig_start(self.tex_list)
def mult_fig_end(self, caption=None):
if caption is not None:
self.caption = caption
mult_fig_end(self.tex_list, self.caption)
self.caption = ""
def include_image(self, fig_name, caption="", label=""):
relative_path = relpath(
self.source_folder.dir_path,
self.save_file.folder.dir_path) + self.source_folder.divider
include_image(self.tex_list, relative_path, fig_name, caption, label)
@cached_property
def view_window(self):
return TEX_Window(agent=self)
def _default_folder(self):
return Folder(
base_dir=
"/Users/thomasaref/Dropbox/Current stuff/Logbook/TA210715A27_cooldown280216",
quality="",
main_dir="Data_0228")
def _default_save_folder(self):
return Folder(
base_dir=
"/Users/thomasaref/Dropbox (Clan Aref)/Current stuff/test_data/Lamb_shift",
main_dir="overall")
def _default_save_file(self):
return Save_TXT(main_file=self.read_file.main_file, folder=Folder(dir_path=self.read_file.folder.dir_path))
def _default_read_file(self):
return Read_TXT(main_file=self.main_file, folder=Folder(dir_path=self.dir_path))
def _default_save_folder(self):
return Folder(
base_dir="/Users/thomasaref/Dropbox/Current stuff/test_data/TA_53",
main_dir="overall")
def _default_folder(self):
return Folder(
base_dir=
"/Users/thomasaref/Dropbox/Current stuff/Logbook/GaAs_sample",
quality="",
main_dir="S11_close_flux")
"""
Created on Thu Feb 11 13:33:17 2016
@author: thomasaref
"""
from taref.tex.tex import TEX
from taref.filer.filer import Folder
from taref.core.shower import shower
from TA53_fundamental import qdt, idt, ideal_qdt, ideal_idt
from taref.filer.read_file import Read_TXT
#/Users/thomasaref/Dropbox (Clan Aref)/Current stuff/Logbook/TA210715A53_cooldown022915/tex_source_files
tx=TEX(source_path=r"/Users/thomasaref/Dropbox/Current stuff/Logbook/TA210715A53_cooldown022915/tex_source_files/TA210715A53_writeup_source.tex")
#"/Users/thomasaref/Dropbox/Current stuff/test_data/source/TA210715A88_source/TA210715A88_writeup.tex")
tx.save_file.file_name="TA210715A53_writeupy"
tx.save_file.folder=Folder(base_dir="/Users/thomasaref/Dropbox/Current stuff/test_data", main_dir="TA_53", quality="")
tx.tex_title="Sample TA210715A53 in Lumi 23-08-16 cooldown"
print tx.source_folder.dir_path
#tx.locals_dict=dict(idt=idt, qdt=qdt)
#sample holder 12
include_all=True
include_text=True
def fft_plots(a, desc=None, label="None", caption="None"):
if desc is None:
desc=a.desc
file_names=Read_TXT(file_path=a.save_file.file_path).read()
tx.mult_fig_start()
for fn in file_names:
if fn!="":