Source Code for Module lib.software.grace

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 15  # GNU General Public License for more details.                                # 
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 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).""" 
 24   
 25  # Python module imports. 
 26  from math import ceil, sqrt 
 27   
 28  # relax module imports. 
 29  import pipe_control 
 30  from pipe_control import pipes 
 31  import specific_analyses 
 32   
 33   
 34 -def write_xy_data(data, file=None, graph_type=None, norm=None): 
 35      """Write the data into the Grace xy-scatter plot. 
 36   
 37      The numerical data should be supplied as a 4 dimensional list or array object.  The first dimension corresponds to the graphs, Gx.  The second corresponds the sets of each graph, Sx.  The third corresponds to the data series (i.e. each data point).  The forth is a list of the information about each point, it is a list where the first element is the x value, the second is the y value, the third is the optional dx or dy error (either dx or dy dependent upon the graph_type arg), and the forth is the optional dy error when graph_type is xydxdy (the third position is then dx). 
 38   
 39   
 40      @param data:            The 4D structure of numerical data to graph (see docstring). 
 41      @type data:             list of lists of lists of float 
 42      @keyword file:          The file object to write the data to. 
 43      @type file:             file object 
 44      @keyword graph_type:    The graph type which can be one of xy, xydy, xydx, or xydxdy. 
 45      @type graph_type:       str 
 46      @keyword norm:          The normalisation flag which if set to True will cause all graphs to be normalised to 1.  The first dimension is the graph. 
 47      @type norm:             None or list of bool 
 48      """ 
 49   
 50      # Graph number. 
 51      graph_num = len(data) 
 52   
 53      # Defaults. 
 54      if not norm: 
 55          norm = [] 
 56          for gi in range(graph_num): 
 57              norm.append(False) 
 58   
 59      # Comment columns. 
 60      comment_col = 2 
 61      if graph_type in ['xydx', 'xydy']: 
 62          comment_col = 3 
 63      elif graph_type == 'xydxdy': 
 64          comment_col = 4 
 65   
 66      # Loop over the graphs. 
 67      for gi in range(graph_num): 
 68          # Loop over the data sets of the graph. 
 69          for si in range(len(data[gi])): 
 70              # The target and type. 
 71              file.write("@target G%s.S%s\n" % (gi, si)) 
 72              file.write("@type %s\n" % graph_type) 
 73   
 74              # Normalisation (to the first data point y value!). 
 75              norm_fact = 1.0 
 76              if norm[gi]: 
 77                  norm_fact = data[gi][si][0][1] 
 78   
 79              # Loop over the data points. 
 80              for point in data[gi][si]: 
 81                  # Bad data. 
 82                  if point[0] == None or point[1] == None: 
 83                      continue 
 84   
 85                  # X and Y data. 
 86                  file.write("%-30s %-30.15f" % (point[0], point[1]/norm_fact)) 
 87   
 88                  # The dx and dy errors. 
 89                  if graph_type in ['xydx', 'xydy', 'xydxdy']: 
 90                      # Catch x or y-axis errors of None. 
 91                      error = point[2] 
 92                      if error == None: 
 93                          error = 0.0 
 94   
 95                      # Write the error. 
 96                      file.write(" %-30.15f" % (error/norm_fact)) 
 97   
 98                  # The dy errors of xydxdy. 
 99                  if graph_type == 'xydxdy': 
100                      # Catch y-axis errors of None. 
101                      error = point[3] 
102                      if error == None: 
103                          error = 0.0 
104   
105                      # Write the error. 
106                      file.write(" %-30.15f" % (error/norm_fact)) 
107   
108                  # The comment if given. 
109                  try: 
110                      file.write("%30s \"# %s\"" % ('', point[comment_col])) 
111                  except IndexError: 
112                      pass 
113   
114                  # End the point. 
115                  file.write("\n") 
116   
117              # End of the data set i. 
118              file.write("&\n") 
119   
120      # Autoscaling of all graphs to avoid user confusion. 
121      for i in range(graph_num): 
122          file.write("@with g%i\n" % i) 
123          file.write("@autoscale\n") 
124   
125      # Auto-arrange the graphs if multiple are present. 
126      if len(data) > 1: 
127          row_num = int(round(sqrt(len(data)))) 
128          col_num = int(ceil(sqrt(len(data)))) 
129          file.write("@arrange(%i, %i, .1, .1, .1, OFF, OFF, OFF)\n" % (row_num, col_num)) 
130   
131   
132 -def write_xy_header(file=None, paper_size='A4', title=None, subtitle=None, view=None, graph_num=1, sets=None, set_names=None, set_colours=None, x_axis_type_zero=None, y_axis_type_zero=None, symbols=None, symbol_sizes=None, symbol_fill=None, linestyle=None, linetype=None, linewidth=None, data_type=None, seq_type=None, axis_labels=None, legend_pos=None, legend=None, norm=None): 
133      """Write the grace header for xy-scatter plots. 
134   
135      Many of these keyword arguments should be supplied in a [X, Y] list format, where the first element corresponds to the X data, and the second the Y data.  Defaults will be used for any non-supplied args (or lists with elements set to None). 
136   
137   
138      @keyword file:                  The file object to write the data to. 
139      @type file:                     file object 
140      @keyword paper_size:            The paper size, i.e. 'A4'.  If set to None, this will default to letter size. 
141      @type paper_size:               str 
142      @keyword title:                 The title of the graph. 
143      @type title:                    None or str 
144      @keyword subtitle:              The sub-title of the graph. 
145      @type subtitle:                 None or str 
146      @keyword view:                  List of 4 coordinates defining the graph view port. 
147      @type view:                     None or list of float 
148      @keyword graph_num:             The total number of graphs. 
149      @type graph_num:                int 
150      @keyword sets:                  The number of data sets in each graph. 
151      @type sets:                     list of int 
152      @keyword set_names:             The names associated with each graph data set Gx.Sy.  For example this can be a list of spin identification strings.  The first dimension is the graph, the second is the set. 
153      @type set_names:                None or list of list of str 
154      @keyword set_colours:           The colours for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
155      @type set_colours:              None or list of list of int 
156      @keyword x_axis_type_zero:      The flags specifying if the X-axis should be placed at zero. 
157      @type x_axis_type_zero:         None or list of lists of bool 
158      @keyword y_axis_type_zero:      The flags specifying if the Y-axis should be placed at zero. 
159      @type y_axis_type_zero:         None or list of lists of bool 
160      @keyword symbols:               The symbol style for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
161      @type symbols:                  None or list of list of int 
162      @keyword symbol_sizes:          The symbol size for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
163      @type symbol_sizes:             None or list of list of int 
164      @keyword symbol_fill:           The symbol file style for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
165      @type symbol_fill:              None or list of list of int 
166      @keyword linestyle:             The line style for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
167      @type linestyle:                None or list of list of int 
168      @keyword linetype:              The line type for each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
169      @type linetype:                 None or list of list of int 
170      @keyword linewidth:             The line width for all elements of each graph data set Gx.Sy.  The first dimension is the graph, the second is the set. 
171      @type linewidth:                None or list of float 
172      @keyword data_type:             The axis data category (in the [X, Y] list format). 
173      @type data_type:                None or list of list of str 
174      @keyword seq_type:              The sequence data type (in the [X, Y] list format).  This is for molecular sequence specific data and can be one of 'res', 'spin', or 'mixed'. 
175      @type seq_type:                 None or list of list of str 
176      @keyword axis_labels:           The labels for the axes (in the [X, Y] list format).  The first dimension is the graph. 
177      @type axis_labels:              None or list of list of str 
178      @keyword legend_pos:            The position of the legend, e.g. [0.3, 0.8].  The first dimension is the graph. 
179      @type legend_pos:               None or list of list of float 
180      @keyword legend:                If True, the legend will be visible.  The first dimension is the graph. 
181      @type legend:                   list of bool 
182      @keyword norm:                  The normalisation flag which if set to True will cause all graphs to be normalised to 1.  The first dimension is the graph. 
183      @type norm:                     list of bool 
184      """ 
185   
186      # Defaults. 
187      if sets == None: 
188          sets = [] 
189          for gi in range(graph_num): 
190              sets.append(1) 
191      if x_axis_type_zero == None: 
192          x_axis_type_zero = [] 
193          for gi in range(graph_num): 
194              x_axis_type_zero.append(False) 
195      if y_axis_type_zero == None: 
196          y_axis_type_zero = [] 
197          for gi in range(graph_num): 
198              y_axis_type_zero.append(False) 
199      if linewidth == None: 
200          linewidth = [] 
201          for gi in range(graph_num): 
202              linewidth.append(0.5) 
203      if norm == None: 
204          norm = [] 
205          for gi in range(graph_num): 
206              norm.append(False) 
207   
208      # Set the None args to lists as needed. 
209      if not data_type: 
210          data_type = [None, None] 
211      if not seq_type: 
212          seq_type = [None, None] 
213      if not axis_labels: 
214          axis_labels = [] 
215          for gi in range(graph_num): 
216              axis_labels.append([None, None]) 
217   
218      # Set the Grace version number of the header's formatting for compatibility. 
219      file.write("@version 50121\n") 
220   
221      # The paper size. 
222      if paper_size == 'A4': 
223          file.write("@page size 842, 595\n") 
224   
225      # Loop over each graph. 
226      for gi in range(graph_num): 
227          # Graph Gi. 
228          file.write("@with g%i\n" % gi) 
229   
230          # The view port. 
231          if not view: 
232              view = [0.15, 0.15, 1.28, 0.85] 
233          file.write("@    view %s, %s, %s, %s\n" % (view[0], view[1], view[2], view[3])) 
234   
235          # The title and subtitle. 
236          if title: 
237              file.write("@    title \"%s\"\n" % title) 
238          if subtitle: 
239              file.write("@    subtitle \"%s\"\n" % subtitle) 
240   
241          # Axis at zero. 
242          if x_axis_type_zero[gi]: 
243              file.write("@    xaxis  type zero true\n") 
244          if y_axis_type_zero[gi]: 
245              file.write("@    yaxis  type zero true\n") 
246   
247          # Axis specific settings. 
248          axes = ['x', 'y'] 
249          for i in range(2): 
250              # Analysis specific methods for making labels. 
251              analysis_spec = False 
252              if pipes.cdp_name(): 
253                  # Flag for making labels. 
254                  analysis_spec = True 
255   
256                  # Specific value and error, conversion factor, and units returning functions. 
257                  return_units = specific_analyses.setup.get_specific_fn('return_units', pipes.get_type()) 
258                  return_grace_string = specific_analyses.setup.get_specific_fn('return_grace_string', pipes.get_type()) 
259   
260                  # Test if the axis data type is a minimisation statistic. 
261                  if data_type[i] and data_type[i] != 'spin' and pipe_control.minimise.return_data_name(data_type[i]): 
262                      return_units = pipe_control.minimise.return_units 
263                      return_grace_string = pipe_control.minimise.return_grace_string 
264   
265              # Some axis default values for spin data. 
266              if data_type[i] == 'spin': 
267                  # Residue only data. 
268                  if seq_type[i] == 'res': 
269                      # X-axis label. 
270                      if not axis_labels[gi][i]: 
271                          axis_labels[gi][i] = "Residue number" 
272   
273                  # Spin only data. 
274                  if seq_type[i] == 'spin': 
275                      # X-axis label. 
276                      if not axis_labels[gi][i]: 
277                          axis_labels[gi][i] = "Spin number" 
278   
279                  # Mixed data. 
280                  if seq_type[i] == 'mixed': 
281                      # X-axis label. 
282                      if not axis_labels[gi][i]: 
283                          axis_labels[gi][i] = "Spin identification string" 
284   
285              # Some axis default values for other data types. 
286              else: 
287                  # Label. 
288                  if analysis_spec and (not axis_labels or not axis_labels[gi][i]): 
289                      # Get the units. 
290                      units = return_units(data_type[i]) 
291   
292                      # Set the label. 
293                      axis_labels[gi][i] = return_grace_string(data_type[i]) 
294   
295                      # Add units. 
296                      if units: 
297                          axis_labels[gi][i] = axis_labels[gi][i] + "\\N (" + units + ")" 
298   
299                      # Normalised data. 
300                      if norm and norm[gi] and axes[i] == 'y': 
301                          axis_labels[gi][i] = axis_labels[gi][i] + " \\N\\q(normalised)\\Q" 
302   
303              # Write out the data. 
304              if axis_labels[gi][i]: 
305                  file.write("@    %saxis  label \"%s\"\n" % (axes[i], axis_labels[gi][i])) 
306              file.write("@    %saxis  label char size 1.00\n" % axes[i]) 
307              file.write("@    %saxis  tick major size 0.50\n" % axes[i]) 
308              file.write("@    %saxis  tick major linewidth %s\n" % (axes[i], linewidth[gi])) 
309              file.write("@    %saxis  tick minor linewidth %s\n" % (axes[i], linewidth[gi])) 
310              file.write("@    %saxis  tick minor size 0.25\n" % axes[i]) 
311              file.write("@    %saxis  ticklabel char size 0.70\n" % axes[i]) 
312   
313          # Legend box. 
314          if legend != None and legend[gi]: 
315              file.write("@    legend on\n") 
316          else: 
317              file.write("@    legend off\n") 
318          if legend_pos != None: 
319              file.write("@    legend %s, %s\n" % (legend_pos[gi][0], legend_pos[gi][1])) 
320   
321          # Frame. 
322          file.write("@    frame linewidth %s\n" % linewidth[gi]) 
323   
324          # Loop over each graph set. 
325          for i in range(sets[gi]): 
326              # Symbol style (default to all different symbols). 
327              if symbols: 
328                  file.write("@    s%i symbol %i\n" % (i, symbols[gi][i])) 
329              else: 
330                  # The symbol number (cycle between 1 and 10). 
331                  num = i % 10 + 1 
332   
333                  # Write out. 
334                  file.write("@    s%i symbol %i\n" % (i, num)) 
335   
336              # Symbol sizes (default to a small size). 
337              if symbol_sizes: 
338                  file.write("@    s%i symbol size %s\n" % (i, symbol_sizes[gi][i])) 
339              else: 
340                  file.write("@    s%i symbol size 0.45\n" % i) 
341   
342              # The symbol fill. 
343              if symbol_fill: 
344                  file.write("@    s%i symbol fill pattern %i\n" % (i, symbol_fill[gi][i])) 
345   
346              # The symbol line width. 
347              file.write("@    s%i symbol linewidth %s\n" % (i, linewidth[gi])) 
348   
349              # Symbol colour (default to nothing). 
350              if set_colours: 
351                  file.write("@    s%i symbol color %s\n" % (i, set_colours[gi][i])) 
352                  file.write("@    s%i symbol fill color %s\n" % (i, set_colours[gi][i])) 
353   
354              # Error bars. 
355              file.write("@    s%i errorbar size 0.5\n" % i) 
356              file.write("@    s%i errorbar linewidth %s\n" % (i, linewidth[gi])) 
357              file.write("@    s%i errorbar riser linewidth %s\n" % (i, linewidth[gi])) 
358   
359              # Line linestyle (default to nothing). 
360              if linestyle: 
361                  file.write("@    s%i line linestyle %s\n" % (i, linestyle[gi][i])) 
362   
363              # Line linetype (default to nothing). 
364              if linetype: 
365                  file.write("@    s%i line type %s\n" % (i, linetype[gi][i])) 
366   
367              # Line and all other colours (default to nothing). 
368              if set_colours: 
369                  file.write("@    s%i line color %s\n" % (i, set_colours[gi][i])) 
370                  file.write("@    s%i fill color %s\n" % (i, set_colours[gi][i])) 
371                  file.write("@    s%i avalue color %s\n" % (i, set_colours[gi][i])) 
372                  file.write("@    s%i errorbar color %s\n" % (i, set_colours[gi][i])) 
373   
374              # Legend. 
375              if set_names and len(set_names) and len(set_names[gi]) and set_names[gi][i]: 
376                  file.write("@    s%i legend \"%s\"\n" % (i, set_names[gi][i])) 
377