rbbt-dm 1.2.6 → 1.2.9

data/lib/rbbt/vector/model.rb

@@ -1,16 +1,25 @@
 require 'rbbt/util/R'
 require 'rbbt/vector/model/util'
+require 'rbbt/util/python'
+
+RbbtPython.add_path Rbbt.python.find(:lib)
+RbbtPython.init_rbbt
 
 class VectorModel
-  attr_accessor :directory, :model_file, :extract_features, :train_model, :eval_model, :post_process
+  attr_accessor :directory, :model_path, :extract_features, :init_model, :train_model, :eval_model, :post_process, :balance
   attr_accessor :features, :names, :labels, :factor_levels
-  attr_accessor :model_options
+  attr_accessor :model, :model_options
 
   def extract_features(&block)
     @extract_features = block if block_given?
     @extract_features
   end
 
+  def init_model(&block)
+    @init_model = block if block_given?
+    @init_model
+  end
+
   def train_model(&block)
     @train_model = block if block_given?
     @train_model
@@ -21,13 +30,17 @@ class VectorModel
     @eval_model
   end
 
+  def init
+    @model ||= self.instance_exec &@init_model
+  end
+
   def post_process(&block)
     @post_process = block if block_given?
     @post_process
   end
 
 
-  def self.R_run(model_file, features, labels, code, names = nil, factor_levels = nil)
+  def self.R_run(model_path, features, labels, code, names = nil, factor_levels = nil)
     TmpFile.with_file do |feature_file|
       Open.write(feature_file, features.collect{|feats| feats * "\t"} * "\n")
       Open.write(feature_file + '.label', labels * "\n" + "\n")
@@ -54,7 +67,7 @@ features = cbind(features, label = labels);
     end
   end
 
-  def self.R_train(model_file, features, labels, code, names = nil, factor_levels = nil)
+  def self.R_train(model_path, features, labels, code, names = nil, factor_levels = nil)
     TmpFile.with_file do |feature_file|
       Open.write(feature_file, features.collect{|feats| feats * "\t"} * "\n")
       Open.write(feature_file + '.label', labels * "\n" + "\n")
@@ -82,13 +95,13 @@ for (c in names(features)){
   if (is.factor(features[[c]]))
     factor_levels[c] = paste(levels(features[[c]]), collapse="\t")
 }
-rbbt.tsv.write("#{model_file}.factor_levels", factor_levels, names=c('Levels'), type='flat')
-save(model, file='#{model_file}')
+rbbt.tsv.write("#{model_path}.factor_levels", factor_levels, names=c('Levels'), type='flat')
+save(model, file='#{model_path}')
       EOF
     end
   end
 
-  def self.R_eval(model_file, features, list, code, names = nil, factor_levels = nil)
+  def self.R_eval(model_path, features, list, code, names = nil, factor_levels = nil)
     TmpFile.with_file do |feature_file|
       if list
         Open.write(feature_file, features.collect{|feat| feat * "\t"} * "\n" + "\n")
@@ -105,7 +118,7 @@ features = read.table("#{ feature_file }", sep ="\\t", stringsAsFactors=TRUE);
 #{ factor_levels.collect do |name,levels|
     "features[['#{name}']] = factor(features[['#{name}']], levels=#{R.ruby2R levels})"
   end * "\n" if factor_levels }
-load(file="#{model_file}");
+load(file="#{model_path}");
 #{code}
 cat(paste(label, sep="\\n", collapse="\\n"));
         EOF
@@ -127,61 +140,77 @@ cat(paste(label, sep="\\n", collapse="\\n"));
     instance_eval code, file
   end
 
-  def initialize(directory = nil, extract_features = nil, train_model = nil, eval_model = nil, post_process = nil, names = nil, factor_levels = nil)
+  def initialize(directory = nil, model_options = {})
     @directory = directory
+    @model_options = IndiferentHash.setup(model_options)
+
     if @directory
-      FileUtils.mkdir_p @directory unless File.exists?(@directory)
+      FileUtils.mkdir_p @directory unless File.exist?(@directory)
+
+      @model_path            = File.join(@directory, "model")
 
-      @model_file = File.join(@directory, "model")
       @extract_features_file = File.join(@directory, "features")
-      @train_model_file = File.join(@directory, "train_model")
-      @eval_model_file = File.join(@directory, "eval_model")
-      @post_process_file = File.join(@directory, "post_process")
-      @train_model_file_R = File.join(@directory, "train_model.R")
-      @eval_model_file_R = File.join(@directory, "eval_model.R")
-      @post_process_file_R = File.join(@directory, "post_process.R")
-      @names_file = File.join(@directory, "feature_names")
-      @levels_file = File.join(@directory, "levels")
-      @options_file = File.join(@directory, "options.json")
-
-      if File.exists?(@options_file)
-        @model_options = JSON.parse(Open.read(@options_file))
+      @init_model_path       = File.join(@directory, "init_model")
+
+      @train_model_path      = File.join(@directory, "train_model")
+      @train_model_path_R    = File.join(@directory, "train_model.R")
+
+      @eval_model_path       = File.join(@directory, "eval_model")
+      @eval_model_path_R     = File.join(@directory, "eval_model.R")
+
+      @post_process_file     = File.join(@directory, "post_process")
+      @post_process_file_R   = File.join(@directory, "post_process.R")
+
+      @names_file            = File.join(@directory, "feature_names")
+      @levels_file           = File.join(@directory, "levels")
+      @options_file          = File.join(@directory, "options.json")
+
+      if File.exist?(@options_file)
+        @model_options = JSON.parse(Open.read(@options_file)).merge(@model_options || {})
         IndiferentHash.setup(@model_options)
       end
     end
-
+    
     if extract_features.nil?
-      if @extract_features_file && File.exists?(@extract_features_file)
+      if @extract_features_file && File.exist?(@extract_features_file)
         @extract_features = __load_method @extract_features_file
       end
     else
       @extract_features = extract_features 
     end
 
+    if init_model.nil?
+      if @init_model_path && File.exist?(@init_model_path)
+        @init_model = __load_method @init_model_path
+      end
+    else
+      @init_model = init_model 
+    end
+
     if train_model.nil?
-      if @train_model_file && File.exists?(@train_model_file)
-        @train_model = __load_method @train_model_file
-      elsif @train_model_file_R && File.exists?(@train_model_file_R)
-        @train_model = Open.read(@train_model_file_R)
+      if @train_model_path && File.exist?(@train_model_path)
+        @train_model = __load_method @train_model_path
+      elsif @train_model_path_R && File.exist?(@train_model_path_R)
+        @train_model = Open.read(@train_model_path_R)
       end
     else
       @train_model = train_model 
     end
 
     if eval_model.nil?
-      if @eval_model_file && File.exists?(@eval_model_file)
-        @eval_model = __load_method @eval_model_file
-      elsif @eval_model_file_R && File.exists?(@eval_model_file_R)
-        @eval_model = Open.read(@eval_model_file_R)
+      if @eval_model_path && File.exist?(@eval_model_path)
+        @eval_model = __load_method @eval_model_path
+      elsif @eval_model_path_R && File.exist?(@eval_model_path_R)
+        @eval_model = Open.read(@eval_model_path_R)
       end
     else
       @eval_model = eval_model
     end
 
     if post_process.nil?
-      if @post_process_file && File.exists?(@post_process_file)
+      if @post_process_file && File.exist?(@post_process_file)
         @post_process = __load_method @post_process_file
-      elsif @post_process_file_R && File.exists?(@post_process_file_R)
+      elsif @post_process_file_R && File.exist?(@post_process_file_R)
         @post_process = Open.read(@post_process_file_R)
       end
     else
@@ -190,7 +219,7 @@ cat(paste(label, sep="\\n", collapse="\\n"));
 
 
     if names.nil?
-      if @names_file && File.exists?(@names_file)
+      if @names_file && File.exist?(@names_file)
         @names = Open.read(@names_file).split("\n")
       end
     else
@@ -198,11 +227,11 @@ cat(paste(label, sep="\\n", collapse="\\n"));
     end
 
     if factor_levels.nil?
-      if @levels_file && File.exists?(@levels_file)
+      if @levels_file && File.exist?(@levels_file)
         @factor_levels = YAML.load(Open.read(@levels_file))
       end
-      if @model_file && File.exists?(@model_file + '.factor_levels')
-        @factor_levels = TSV.open(@model_file + '.factor_levels')
+      if @model_path && File.exist?(@model_path + '.factor_levels')
+        @factor_levels = TSV.open(@model_path + '.factor_levels')
       end
     else
       @factor_levels = factor_levels 
@@ -241,23 +270,24 @@ cat(paste(label, sep="\\n", collapse="\\n"));
     case 
     when Proc === train_model
       begin
-        Open.write(@train_model_file, train_model.source)
+        Open.write(@train_model_path, train_model.source)
       rescue
       end
     when String === train_model
-      Open.write(@train_model_file_R, @train_model)
+      Open.write(@train_model_path_R, @train_model)
     end
 
     Open.write(@extract_features_file, @extract_features.source) if @extract_features
+    Open.write(@init_model_path, @init_model.source) if @init_model
 
     case 
     when Proc === eval_model
       begin
-        Open.write(@eval_model_file, eval_model.source)
+        Open.write(@eval_model_path, eval_model.source)
       rescue
       end
     when String === eval_model
-      Open.write(@eval_model_file_R, eval_model)
+      Open.write(@eval_model_path_R, eval_model)
     end
 
     case 
@@ -270,24 +300,37 @@ cat(paste(label, sep="\\n", collapse="\\n"));
       Open.write(@post_process_file_R, post_process)
     end
 
-
     Open.write(@levels_file, @factor_levels.to_yaml) if @factor_levels
     Open.write(@names_file, @names * "\n" + "\n") if @names
     Open.write(@options_file, @model_options.to_json) if @model_options
   end
 
   def train
-    case 
-    when Proc === @train_model
-      self.instance_exec(@model_file, @features, @labels, @names, @factor_levels, &@train_model)
-    when String === @train_model
-      VectorModel.R_train(@model_file,  @features, @labels, train_model, @names, @factor_levels)
+    begin
+      if @balance
+        @original_features = @features
+        @original_labels = @labels
+        self.balance_labels
+      end
+
+      case 
+      when Proc === @train_model
+        self.instance_exec(@features, @labels, @names, @factor_levels, &@train_model)
+      when String === @train_model
+        VectorModel.R_train(@model_path, @features, @labels, train_model, @names, @factor_levels)
+      end
+    ensure
+      if @balance
+        @features =  @original_features
+        @labels = @original_labels
+      end
     end
+
     save_models if @directory
   end
 
   def run(code)
-    VectorModel.R_run(@model_file,  @features, @labels, code, @names, @factor_levels)
+    VectorModel.R_run(@model_path,  @features, @labels, code, @names, @factor_levels)
   end
 
   def eval(element)
@@ -295,14 +338,14 @@ cat(paste(label, sep="\\n", collapse="\\n"));
 
     result = case 
              when Proc === @eval_model
-               self.instance_exec(@model_file, features, false, nil, @names, @factor_levels, &@eval_model)
+               self.instance_exec(features, false, nil, @names, @factor_levels, &@eval_model)
              when String === @eval_model
-               VectorModel.R_eval(@model_file, features, false, eval_model, @names, @factor_levels)
+               VectorModel.R_eval(@model_path, features, false, eval_model, @names, @factor_levels)
              else
                raise "No @eval_model function or R script"
              end
 
-    result = self.instance_exec(result, &@post_process) if Proc === @post_process 
+    result = self.instance_exec(result, false, &@post_process) if Proc === @post_process 
 
     result
   end
@@ -321,12 +364,12 @@ cat(paste(label, sep="\\n", collapse="\\n"));
 
     result = case 
              when Proc === eval_model
-               self.instance_exec(@model_file, features, true, nil, @names, @factor_levels, &@eval_model)
+               self.instance_exec(features, true, nil, @names, @factor_levels, &@eval_model)
              when String === eval_model
-               VectorModel.R_eval(@model_file, features, true, eval_model, @names, @factor_levels)
+               VectorModel.R_eval(@model_path, features, true, eval_model, @names, @factor_levels)
              end
 
-    result = self.instance_exec(result, &@post_process) if Proc === @post_process 
+    result = self.instance_exec(result, true, &@post_process) if Proc === @post_process 
 
     result
   end
@@ -438,6 +481,7 @@ cat(paste(label, sep="\\n", collapse="\\n"));
       @features = orig_features
       @labels = orig_labels
     end unless folds == -1
+
     self.reset_model if self.respond_to? :reset_model
     self.train unless folds == 1
     res

data/python/rbbt_dm/__init__.py

@@ -1 +1,48 @@
-# Keep
+from torch.utils.data import Dataset, DataLoader
+
+class TSVDataset(Dataset):
+    def __init__(self, tsv):
+        self.tsv = tsv
+
+    def __getitem__(self, key):
+        if (type(key) == int):
+            row = self.tsv.iloc[key]
+        else:
+            row = self.tsv.loc[key]
+
+        row = row.to_numpy()
+        features = row[:-1]
+        label = row[-1]
+
+        return features, label
+
+    def __len__(self):
+        return len(self.tsv)
+
+def tsv_dataset(filename, *args, **kwargs):
+    import rbbt
+    return TSVDataset(rbbt.tsv(filename, *args, **kwargs))
+
+def tsv(*args, **kwargs):
+    return tsv_dataset(*args, **kwargs)
+
+def data_dir():
+    import rbbt
+    return rbbt.path('var/rbbt_dm/data')
+
+if __name__ == "__main__":
+    import rbbt
+
+    filename = "/home/miki/test/numeric.tsv"
+    ds = tsv(filename)
+
+    dl = DataLoader(ds, batch_size=1)
+
+    for f, l in iter(dl):
+        print(".")
+        print(f[0,:])
+        print(l[0])
+
+
+
+

data/python/rbbt_dm/atcold/plot_lib.py

@@ -0,0 +1,141 @@
+from matplotlib import pyplot as plt
+import numpy as np
+import torch
+from IPython.display import HTML, display
+
+
+def set_default(figsize=(10, 10), dpi=100):
+    plt.style.use(['dark_background', 'bmh'])
+    plt.rc('axes', facecolor='k')
+    plt.rc('figure', facecolor='k')
+    plt.rc('figure', figsize=figsize, dpi=dpi)
+
+
+def plot_data(X, y, d=0, auto=False, zoom=1):
+    X = X.cpu()
+    y = y.cpu()
+    plt.scatter(X.numpy()[:, 0], X.numpy()[:, 1], c=y, s=20, cmap=plt.cm.Spectral)
+    plt.axis('square')
+    plt.axis(np.array((-1.1, 1.1, -1.1, 1.1)) * zoom)
+    if auto is True: plt.axis('equal')
+    plt.axis('off')
+
+    _m, _c = 0, '.15'
+    plt.axvline(0, ymin=_m, color=_c, lw=1, zorder=0)
+    plt.axhline(0, xmin=_m, color=_c, lw=1, zorder=0)
+
+
+def plot_model(X, y, model):
+    model.cpu()
+    mesh = np.arange(-1.1, 1.1, 0.01)
+    xx, yy = np.meshgrid(mesh, mesh)
+    with torch.no_grad():
+        data = torch.from_numpy(np.vstack((xx.reshape(-1), yy.reshape(-1))).T).float()
+        Z = model(data).detach()
+    Z = np.argmax(Z, axis=1).reshape(xx.shape)
+    plt.contourf(xx, yy, Z, cmap=plt.cm.Spectral, alpha=0.3)
+    plot_data(X, y)
+
+
+def show_scatterplot(X, colors, title=''):
+    colors = colors.cpu().numpy()
+    X = X.cpu().numpy()
+    plt.figure()
+    plt.axis('equal')
+    plt.scatter(X[:, 0], X[:, 1], c=colors, s=30)
+    # plt.grid(True)
+    plt.title(title)
+    plt.axis('off')
+
+
+def plot_bases(bases, width=0.04):
+    bases = bases.cpu()
+    bases[2:] -= bases[:2]
+    plt.arrow(*bases[0], *bases[2], width=width, color=(1,0,0), zorder=10, alpha=1., length_includes_head=True)
+    plt.arrow(*bases[1], *bases[3], width=width, color=(0,1,0), zorder=10, alpha=1., length_includes_head=True)
+
+
+def show_mat(mat, vect, prod, threshold=-1):
+    # Subplot grid definition
+    fig, (ax1, ax2, ax3) = plt.subplots(1, 3, sharex=False, sharey=True,
+                                        gridspec_kw={'width_ratios':[5,1,1]})
+    # Plot matrices
+    cax1 = ax1.matshow(mat.numpy(), clim=(-1, 1))
+    ax2.matshow(vect.numpy(), clim=(-1, 1))
+    cax3 = ax3.matshow(prod.numpy(), clim=(threshold, 1))
+
+    # Set titles
+    ax1.set_title(f'A: {mat.size(0)} \u00D7 {mat.size(1)}')
+    ax2.set_title(f'a^(i): {vect.numel()}')
+    ax3.set_title(f'p: {prod.numel()}')
+
+    # Remove xticks for vectors
+    ax2.set_xticks(tuple())
+    ax3.set_xticks(tuple())
+    
+    # Plot colourbars
+    fig.colorbar(cax1, ax=ax2)
+    fig.colorbar(cax3, ax=ax3)
+
+    # Fix y-axis limits
+    ax1.set_ylim(bottom=max(len(prod), len(vect)) - 0.5)
+
+
+colors = dict(
+    aqua='#8dd3c7',
+    yellow='#ffffb3',
+    lavender='#bebada',
+    red='#fb8072',
+    blue='#80b1d3',
+    orange='#fdb462',
+    green='#b3de69',
+    pink='#fccde5',
+    grey='#d9d9d9',
+    violet='#bc80bd',
+    unk1='#ccebc5',
+    unk2='#ffed6f',
+)
+
+
+def _cstr(s, color='black'):
+    if s == ' ':
+        return f'<text style=color:#000;padding-left:10px;background-color:{color}> </text>'
+    else:
+        return f'<text style=color:#000;background-color:{color}>{s} </text>'
+
+# print html
+def _print_color(t):
+    display(HTML(''.join([_cstr(ti, color=ci) for ti, ci in t])))
+
+# get appropriate color for value
+def _get_clr(value):
+    colors = ('#85c2e1', '#89c4e2', '#95cae5', '#99cce6', '#a1d0e8',
+              '#b2d9ec', '#baddee', '#c2e1f0', '#eff7fb', '#f9e8e8',
+              '#f9e8e8', '#f9d4d4', '#f9bdbd', '#f8a8a8', '#f68f8f',
+              '#f47676', '#f45f5f', '#f34343', '#f33b3b', '#f42e2e')
+    value = int((value * 100) / 5)
+    if value == len(colors): value -= 1  # fixing bugs...
+    return colors[value]
+
+def _visualise_values(output_values, result_list):
+    text_colours = []
+    for i in range(len(output_values)):
+        text = (result_list[i], _get_clr(output_values[i]))
+        text_colours.append(text)
+    _print_color(text_colours)
+
+def print_colourbar():
+    color_range = torch.linspace(-2.5, 2.5, 20)
+    to_print = [(f'{x:.2f}', _get_clr((x+2.5)/5)) for x in color_range]
+    _print_color(to_print)
+
+
+# Let's only focus on the last time step for now
+# First, the cell state (Long term memory)
+def plot_state(data, state, b, decoder):
+    actual_data = decoder(data[b, :, :].numpy())
+    seq_len = len(actual_data)
+    seq_len_w_pad = len(state)
+    for s in range(state.size(2)):
+        states = torch.sigmoid(state[:, b, s])
+        _visualise_values(states[seq_len_w_pad - seq_len:], list(actual_data))

data/python/rbbt_dm/atcold/spiral.py

@@ -0,0 +1,27 @@
+import torch
+import math
+def spiral_data(N=1000, D=2, C=3):
+    X = torch.zeros(N * C, D)
+    y = torch.zeros(N * C, dtype=torch.long)
+    for c in range(C):
+        index = 0
+        t = torch.linspace(0, 1, N)
+        # When c = 0 and t = 0: start of linspace
+        # When c = 0 and t = 1: end of linpace
+        # This inner_var is for the formula inside sin() and cos() like sin(inner_var) and cos(inner_Var)
+        inner_var = torch.linspace(
+            # When t = 0
+            (2 * math.pi / C) * (c),
+            # When t = 1
+            (2 * math.pi / C) * (2 + c),
+            N
+        ) + torch.randn(N) * 0.2
+
+        for ix in range(N * c, N * (c + 1)):
+            X[ix] = t[index] * torch.FloatTensor((
+                math.sin(inner_var[index]), math.cos(inner_var[index])
+            ))
+            y[ix] = c
+            index += 1
+
+    return (X, y)