Readers

Collection of functions to read simulation data and other files needed by MIMBSimUtils.

Readers.readChemField(simid, t, indir, fieldname, gzipped=True, border=True)[source]

Read chemical field from file.

Parameters:
  • simid (str) – simulation identifier
  • t (int) – time step
  • indir (str) – path to data files
  • fieldname (str) – name of the chemical field
  • gzipped (bool) – data is gzipped (gzipped data is expected to be in indir/simid/)
  • border (bool) – cut of border pixels
Returns:

numpy array with the levels of the chemical field at each position

Readers.readColorMap(filename)[source]

Read colormap from a file, formatted like: celltype r g b

Parameters:filename (str) – file with the colormap
Returns:dictionary with cell type as keys and colors (r,g,b) as values.
Readers.readSigma(simid, t, indir, gzipped=True, border=True)[source]

Read cell field (sigma) from file.

Parameters:
  • simid (str) – simulation identifier
  • t (int) – time step
  • indir (str) – path to data files
  • gzipped (bool) – data is gzipped (gzipped data is expected to be in indir/simid/)
  • border (bool) – cut of border pixels
Returns:

numpy array with cell id’s

Readers.readTau(simid, t, indir, gzipped=True, border=True)[source]

Read type field (tau) from file.

Parameters:
  • simid (str) – simulation identifier
  • t (int) – time step
  • indir (str) – path to data files
  • gzipped (bool) – data is gzipped (gzipped data is expected to be in indir/simid/)
  • border (bool) – cut of border pixels
Returns:

numpy array with cell types

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