update

README.md

@@ -31,16 +31,16 @@ For local installation, clone the repository from GitHub and then install it usi
 ```shell
 git clone https://github.com/JintaoLee-Roger/cigvis.git
 # Minimal installation
-pip install -e .
+pip install -e . --config-settings editable_mode=strict
 
 # include plotly 
-pip install -e ".[plotly]"
+pip install -e ".[plotly]" --config-settings editable_mode=strict
 
 # include viser
-pip install -e ".[viser]"
+pip install -e ".[viser]" --config-settings editable_mode=strict
 
 # install all dependencies
-pip install -e ".[all]"
+pip install -e ".[all]" --config-settings editable_mode=strict
 ```
 
 ## Core Features

changelog.md

@@ -1,6 +1,12 @@
 # Changelog
 
 
+### v0.1.2
+
+- added `blue_white_purple` colormap
+- added `nancolor` to set nan color in viser
+- added `extract_arbitrary_line_by_view` function to a extract arbitrary line by clicking
+
 
 ### v0.1.1
 

cigvis/colormap.py

@@ -29,11 +29,13 @@
 from .customcmap import *
 
 
-def arrs_to_image(arr, cmap, clim, as_uint8=False):
+def arrs_to_image(arr, cmap, clim, as_uint8=False, nancolor=None):
 
-    def _to_image(arr, cmap, clim):
+    def _to_image(arr, cmap, clim, nancolor=None):
         norm = plt.Normalize(vmin=clim[0], vmax=clim[1])
         cmap = cmap_to_mpl(cmap)
+        if nancolor is not None:
+            cmap.set_bad(nancolor)
         img = cmap(norm(arr))
         return img
 
@@ -46,9 +48,9 @@ def _to_image(arr, cmap, clim):
     if len(arr) != len(cmap) or len(arr) != len(clim):
         raise RuntimeError("(len(arr) != len(cmap)) or (len(arr) != len(clim))")
 
-    out = _to_image(arr[0], cmap[0], clim[0])
+    out = _to_image(arr[0], cmap[0], clim[0], nancolor)
     for i in range(1, len(arr)):
-        img = _to_image(arr[i], cmap[i], clim[i])
+        img = _to_image(arr[i], cmap[i], clim[i], nancolor)
 
         bgRGB = out[:, :, :3]
         fgRGB = img[:, :, :3]

cigvis/gui/custom_widgets.py

@@ -259,7 +259,7 @@ def __init__(self, interps=None, parent=None) -> None:
         colormap_label = qtw.QLabel('cmap:')
         self.colormap_combo = EditableComboBox()
         colormaps = [
-            'gray', 'seismic', 'Petrel', 'stratum', 'jet', 'od_seismic1',
+            'gray', 'seismic', 'Petrel', 'stratum', 'jet', 'od_seismic1', 'bwp',
             'od_seismic2', 'od_seismic3'
         ]
         self.colormap_combo.addItems(colormaps)

cigvis/gui/gui2d/control_panel.py

@@ -320,12 +320,18 @@ def __init__(self,
         row_tab.addWidget(self.tab_widget)
         row_tab.setStretch(0, 1)
 
+        value_tab = qtw.QHBoxLayout()
+        self.status_label = qtw.QLabel('')
+        self.status_label.setStyleSheet("font-size: 12px; padding: 5px;")
+        value_tab.addWidget(self.status_label)
+
         self.addlayout(layout, [
             row1_layout,
             row_folder,
             row2_layout,
             rowl_layout,
             row_tab,
+            value_tab,
         ])
 
         layout.addStretch(1)

cigvis/gui/gui2d/plot_canvas.py

@@ -272,6 +272,11 @@ def on_mouse_move(self, event):
                                            self.scrib_list[-1][1])
             self.draw()
 
+        if event.inaxes and self.data is not None:
+            v = self.data[round(event.xdata), round(event.ydata)]
+            self.parent().parent().controlP.status_label.setText(
+                f'x={event.xdata:.1f}, y={event.ydata:.1f}, v={v:.1f}')
+
     def on_mouse_release(self, event):
         if self.box_mode > 0 and event.inaxes:
             self.rect = None
@@ -359,7 +364,7 @@ def __init__(self, parent=None, width=5, height=4, dpi=100):
         self.fig = Figure(figsize=(width, height), dpi=dpi)
         self.axes = self.fig.add_subplot(111)
         self.axes.set_axis_off()
-        self.fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
+        self.fig.subplots_adjust(left=0.08, right=0.98, top=0.98, bottom=0.05)
         super().__init__(self.fig)
         self.setParent(parent)
         self.controlP = self.parent().controlP
@@ -408,7 +413,9 @@ def plot(self):
             self.axes.axis('off')
             self.baseim = None
         else:
-            self.baseim = self.axes.imshow(self.data.T, **self.params)
+            self.baseim = self.axes.imshow(self.data.T,
+                                           **self.params,
+                                           aspect='auto')
         self.draw()
 
     def clear(self):

cigvis/tools.py

@@ -0,0 +1,127 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from cigvis.utils.surfaceutils import arbitray_line
+
+
+def extract_arbitrary_line_by_view(data: np.ndarray,
+                                   bmap: str = 'data',
+                                   draw_arb: bool = True,
+                                   *,
+                                   line: bool = True,
+                                   idx: int = 50,
+                                   cline='#F3AA3C'):
+    """
+    extract arbitrary line from seismic data by clicking
+
+    Parameters
+    ----------
+    - data: np.ndarray 
+        3D seismic data
+    - bmap: str
+        background map, 'data' or 'blank'
+    - line : bool
+        whether to draw the broken line 
+    - idx: int 
+        the slice index of the seismic data if bmap is 'data'
+    - cline: str
+        color of the line
+
+    Returns
+    -------
+    - out: np.ndarray
+        extracted arbitrary line
+    - p: np.ndarray
+        extracted arbitrary line path
+    - coords: np.ndarray
+        the coordinates by clicking
+    """
+    fig, ax = plt.subplots()
+    if bmap == 'data':
+        img = data[:, :, idx]
+        ax.imshow(img.T, cmap='gray', aspect='auto')
+    else:
+        img = np.zeros((data.shape[1], data.shape[0], 4), dtype=np.uint8)
+        img = img + int(0.9 * 255)
+        ax.imshow(img, aspect='auto')
+        ax.grid(True)
+
+    ax.set_title('Obtain a path by clicking, press "u" to undo, "enter" to finish') # yapf: disable
+    ax.set_xlabel('Inline')
+    ax.set_ylabel('Crossline')
+    coords = []
+    lines = []
+    points = []
+    out = None
+    p = None
+    indices = None
+
+    def _draw_arbline():
+        if (len(coords) > 0):
+            ax.clear()
+            nonlocal out, p, indices
+            out, p, indices = arbitray_line(data, coords)
+            ax.grid(False)
+            ax.imshow(out.T, cmap='gray', aspect='auto')
+            if line:
+                for i in range(len(indices)):
+                    ax.plot([indices[i]] * out.shape[1],
+                            range(out.shape[1]),
+                            'w--',
+                            lw=0.5)
+                    if i > 0 and i < len(indices) - 1:
+                        ax.text(indices[i] - out.shape[0] / 50,
+                                30,
+                                str(indices[i]),
+                                color='w',
+                                fontsize=10)
+            ax.set_title("Arbitrary Line")
+            ax.set_ylabel('Time')
+            fig.canvas.draw()
+            # plt.close()
+
+    def _click_event(event):
+        if event.inaxes:
+            coords.append((round(event.xdata, 2), round(event.ydata, 2)))
+            p = ax.plot(event.xdata, event.ydata, 'ro')[0]
+            points.append(p)
+            if len(coords) > 1:
+                x_coords, y_coords = zip(*coords[-2:])
+                line, = ax.plot(x_coords, y_coords, c=cline)
+                lines.append(line)
+            fig.canvas.draw()
+
+    def _undo_last(event):
+        if event.key == 'u':
+            if coords:
+                coords.pop()
+                p = points.pop()
+                p.remove()
+                if len(lines) > 0:
+                    l = lines.pop()
+                    l.remove()
+                fig.canvas.draw()
+        if event.key in ('enter', 'return', 'escape'):
+            if draw_arb:
+                fig.canvas.mpl_disconnect(cid_click)
+                fig.canvas.mpl_disconnect(cid_key)
+                _draw_arbline()
+            else:
+                plt.close(fig)
+
+    cid_click = fig.canvas.mpl_connect('button_press_event', _click_event)
+    cid_key = fig.canvas.mpl_connect('key_press_event', _undo_last)
+
+    plt.show()
+
+    return out, p, indices, np.array(coords)
+
+
+if __name__ == '__main__':
+    from cigsegy import SegyNP
+    d = SegyNP('/Volumes/T7/DATA/cnooc_bj/data/FEF.segy')
+    out, p, ind, c = extract_arbitrary_line_by_view(
+        d,
+        bmap='data',
+        draw_arb=True,
+    )
+    print(c.shape)

cigvis/utils/surfaceutils.py

@@ -231,8 +231,6 @@ def interp_surf(volume: np.ndarray,
     return out
 
 
-
-
 def interp_arb(p: np.ndarray, d: np.ndarray) -> np.ndarray:
     """
     Interpolates a 1d series in 3d space by **linear** interpolation.
@@ -253,10 +251,9 @@ def interp_arb(p: np.ndarray, d: np.ndarray) -> np.ndarray:
     f11 = d[:, 3, :]
 
     # linear interpolation
-    out = (f00 * (1 - x)[:, None] * (1 - y)[:, None] + 
-           f01 * (1 - x)[:, None] * y[:, None] + 
-           f10 * x[:, None] * (1 - y)[:, None] + 
-           f11 * x[:, None] * y[:, None])
+    out = (f00 * (1 - x)[:, None] * (1 - y)[:, None] + f01 *
+           (1 - x)[:, None] * y[:, None] + f10 * x[:, None] *
+           (1 - y)[:, None] + f11 * x[:, None] * y[:, None])
 
     return out
 
@@ -276,8 +273,9 @@ def interpolate_path(points, di=1):
     x_points = np.interp(distances_interp, cum_distances, points[:, 0])
     y_points = np.interp(distances_interp, cum_distances, points[:, 1])
 
-    return np.column_stack((x_points, y_points))
+    indices = np.searchsorted(distances_interp, cum_distances)
 
+    return np.column_stack((x_points, y_points)), indices
 
 
 def extract_data(data, p):
@@ -324,19 +322,17 @@ def extract_data(data, p):
     unique, inverse = np.unique(all_points, axis=0, return_inverse=True)
     unique_data = np.array([data[i, j] for i, j in unique])
 
-
     return pout, unique_data[inverse].reshape(N, 4, n3)
 
 
-
 def arbitray_line(data, points, di: float = 1):
     """
     data : SegyNP or np.ndarray
     points : the points to interpolate a path
     di : step
     """
-    p = interpolate_path(points, di)
+    p, indices = interpolate_path(points, di)
     pout, pdata = extract_data(data, p)
     out = interp_arb(pout, pdata)
 
-    return out, p
+    return out, p, indices

cigvis/visernodes/volume_slice.py

@@ -20,7 +20,8 @@ def __init__(self,
                  pos=0,
                  cmap='gray',
                  clim=None,
-                 scale=-1):
+                 scale=-1,
+                 nancolor=None):
         self._server = None # viser.ViserServer
         self.volume = volume
         self.axis = axis
@@ -31,6 +32,7 @@ def __init__(self,
         ]
 
         self.init_scale = [8 / max(volume.shape)] * 3
+        self.nancolor = nancolor
 
         if isinstance(scale, (int, float)):
             if scale < 0:
@@ -105,7 +107,7 @@ def to_img(self):
             fg = [mask[:, :, self.pos] for mask in self.masks]
 
         img = colormap.arrs_to_image([bg] + fg, [self.cmap] + self.fg_cmaps,
-                                     [self.clim] + self.fg_clims, True)
+                                     [self.clim] + self.fg_clims, True, self.nancolor)
         return img
 
     def update_node(self, pos):