Fix APs and display stack

Notebooks/APs.ipynb

@@ -157,7 +157,7 @@
     "sd   = np.array([0.5,0.9,0.99,0.999])#,1e4,1e5,5e5])\n",
     "moi  = np.array([0.01,0.02,0.03,0.04,0.05,0.06,0.07,0.08,0.09,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.99])\n",
     "\n",
-    "t = triskele.Triskele(layers_stack[:,:,0], verbose=False)\n",
+    "t = triskele.Triskele(layers_stack[:,:,:2], verbose=False)\n",
     "attributes_min = t.filter(tree='min-tree',\n",
     "                      area=area,\n",
     "                      standard_deviation=sd,\n",

Notebooks/Node Streaming Benchmark.ipynb

@@ -24,15 +24,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "load = ld2dap.LoadTIFF(('../Data/test.tiff', '../Data/test2.tiff'))\n",
+    "load = ld2dap.LoadTIFF('../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif')\n",
     "trsh = ld2dap.Treshold(1e4)\n",
-    "aps  = ld2dap.AttributeProfiles(area=[100, 1e3, 1e4])\n",
+    "aps  = ld2dap.AttributeProfiles(area=[1e6], moi=[.5])\n",
-    "aps2 = ld2dap.AttributeProfiles(area=[100, 1e3, 1e4])\n",
     "\n",
-    "disp = ld2dap.ShowFig(fname=None)\n",
+    "disp = ld2dap.ShowFig('all')\n",
     "out  = ld2dap.RawOutput()\n",
     "\n",
-    "aps2.input = aps\n",
     "out.input  = aps\n",
     "disp.input = aps\n",
     "aps.input  = trsh\n",
@@ -41,6 +39,15 @@
     "disp.run()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "' > '.join(x if x is not None else '' for x in out.metadata[0].desc[3])"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -50,14 +57,20 @@
     "out.data.shape"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "for i, m in enumerate(out.metadata):\n",
+    "print(out.metadata[1])"
-    "    print('{}: {}'.format(i, m))"
    ]
   },
   {
@@ -66,7 +79,27 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "load.files"
+    "' > '.join(filter(None, out.metadata[0].desc[3]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for x in out.metadata[0].desc:\n",
+    "    print (x)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for i, m in enumerate(out.metadata):\n",
+    "    print('{}: {}'.format(i, m))"
    ]
   },
   {

ld2dap/AttributeProfiles.py

@@ -43,6 +43,13 @@ class AttributeProfiles(Filter):
             att_offset[att] = len(values) * 2 + 1 if values is not None else 0
         return att_offset
 
+    def _process_len(self):
+        att_len = dict()
+        for att in ['area', 'sd', 'moi']:
+            values = self.__getattribute__(att)
+            att_len[att] = len(values) if values is not None else 0
+        return att_len
+
     def _process(self, data, metadata):
         t       = triskele.Triskele(data, verbose=False)
         att_min = t.filter(tree='min-tree', area=self.area,
@@ -58,23 +65,35 @@ class AttributeProfiles(Filter):
         ### Pre-process descriptions
         att_desc = self._process_desc()
 
-        ### Compute stack offsets
+        ### Compute stack offsets and att length
+        att_len    = self._process_len()
         att_offset = self._process_offset()
         stack_offset = sum(att_offset.values())
 
         ### Merge old and new descriptions
         metadata_new = list()
+        ### Re-order to create original APs
+        raster_list  = list()
         for stack in metadata:
             if stack.end - stack.begin > 1:
                 raise NotImplementedError('Nested filtering not implemented yet')
 
+            do = dso = 0
             for att in ['area', 'sd', 'moi']:
                 if att_offset[att] == 0:
                     continue
 
-                stack_new = Stack(stack_offset * stack.begin, att_offset[att],
+                al = att_len[att]
+                raster_list.append(att_min[:,:,do+al:do:-1])
+                raster_list.append(att_min[:,:,0])
+                raster_list.append(att_max[:,:,do+1:do+al+1])
+                do += al
+
+                stack_new = Stack(dso + stack_offset * stack.begin, att_offset[att],
                         stack.desc[0], stack.symb[0])
 
+                dso += att_offset[att]
+
                 for old_desc, new_desc in zip(stack_new.desc, att_desc[att]):
                     print('DESCRIPTION: {} > {}'.format(old_desc, new_desc))
                     old_desc.append(new_desc)
@@ -82,9 +101,9 @@ class AttributeProfiles(Filter):
                 metadata_new.append(stack_new)
 
 
-        att = np.dstack((att_min, att_max))
+        data_new = np.dstack(raster_list)
 
-        return att, metadata_new
+        return data_new, metadata_new
 
 if __name__ == '__main__':
     area = [10, 100, 1000]

ld2dap/ShowFig.py

@@ -13,20 +13,32 @@ from ld2dap.core import Output
 import matplotlib.pyplot as plt
 
 class ShowFig(Output):
-    def __init__(self, fname, bbox_inches='tight', pad_inches=1):
+    def __init__(self, stack_id=0, bbox_inches='tight', pad_inches=1):
         super().__init__(self.__class__.__name__)
-        self.fname       = fname
         self.bbox_inches = bbox_inches
         self.pad_inches  = pad_inches
+        self.stack_id    = stack_id
 
     def _process(self, data, metadata):
+        if self.stack_id == 'all':
+            for stack in metadata:
+                self._showfig(data, stack)
+        else:
+            stack = metadata[self.stack_id]
+            self._showfig(data, stack)
+
+    def _showfig(self, data, stack):
+        fig_count = stack.end - stack.begin
+
         im_size = 2
-        fig = plt.figure(figsize=(16*im_size,3*im_size))
+        fig = plt.figure(figsize=(16*im_size,3*im_size*fig_count))
-        f1 = fig.add_subplot(111)
+
-        img = f1.imshow(data[:,:,-1])
+        for i, di in enumerate(range(stack.begin, stack.end)):
-        plt.colorbar(img)
+            f1 = fig.add_subplot(fig_count, 1, i + 1)
-        if metadata is not None:
+            img = f1.imshow(data[:,:,di])
-            print (metadata[0].desc)
+            plt.colorbar(img)
-            f1.set_title(' > '.join(metadata[0].desc[-1]))
+            f1.set_title(' > '.join(filter(None, stack.desc[i])))
+
         plt.show()
         plt.close(fig)
+