Merge pull request #5 from JintaoLee-Roger/dev

v1.1.7

.gitignore

@@ -24,6 +24,7 @@ _doxygenxml
 docs/cigsegy
 segyfile
 __pycache__
+todo.txt
 
 test.*
 thridpart/

CMakeLists.txt

@@ -24,7 +24,7 @@ ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 message("Install Prefix: " ${CMAKE_INSTALL_PREFIX})
 
 set(BUILD_PYTHON ON)
-set(BUILD_TOOLS ON)
+set(BUILD_TOOLS OFF)
 set(ENABLE_OPENMP OFF)
 set(BUILD_TEST OFF)
 

README.rst

@@ -83,17 +83,11 @@ intervals, data format ...
 .. Note::
 
     If you are unsure about the values of some parameters, 
-    you can use the default values, such as
+    you can ignore them and cigsegy will try to guess them automatically.
 
     .. code-block:: python
 
-        >>> cigsegy.metaInfo('fx.segy', iline=9, xline=21)
-
-    You also can set ``use_guess=True`` to use the guessed parameters:
-
-    .. code-block:: python
-
-        >>> cigsegy.metaInfo('rogan.sgy', use_guess=True)
+        >>> cigsegy.metaInfo('fx.segy', iline=9, xline=21) # ignore istep, xstep, ...
 
 
 4. Read the SEG-Y
@@ -139,6 +133,25 @@ There is often such a workflow:
     # d is a numpy array, d.shape == (n-inlines, n-crosslines, n-time)
     >>> cigsegy.create('out.segy', d, format=5, start_time=0, iline_interval=15, ...)
 
+
+7. Access the SEG-Y file as a 3D numpy array, without reading the whole file into memory
+
+.. code-block:: python
+
+    >>> from cigsegy import SegyNP
+    >>> d = SegyNP('rogan.sgy', iline=9, xline=21)
+    >>> d.shape # (ni, nx, nt), use as a numpy array, 3D geometry
+    >> sx = d[100] # the 100-th inline profile
+    >> sx = d[100:200] # return a 3D array with shape (100, nx, nt)
+    >> sx = d[:, 200, :] # the 200-th crossline profile
+    >> sx = d[:, :, 100] # the 100-th time slice, note, it may be slow if the file is large
+    >> sx.min(), sx.max() 
+    # get the min and max value, but they are evaluated from a part of data, 
+    # so they may not be the real min and max value
+    >> sx.trace_cout # get the number of traces for the file
+
+
+
 License
 =======
 
@@ -151,6 +164,29 @@ TODO
 - Add convenient function to support **unsorted** prestack gathers.
 
 
+Citations
+===========
+If you find this work useful in your research and want to cite it, please consider use this:
+
+Plain Text
+
+.. code-block:: python
+
+    Li, Jintao. "CIGSEGY: A tool for exchanging data between SEG-Y format and NumPy array inside Python environment". URL: https://github.com/JintaoLee-Roger/cigsegy
+
+
+BibTex
+
+.. code-block:: latex
+
+    @misc{cigsegy,
+    author = {Li, Jintao},
+    title = {CIGSEGY: A tool for exchanging data between SEG-Y format and NumPy array inside Python environment},
+    url = {\url{https://github.com/JintaoLee-Roger/cigsegy}},
+    }
+
+
+
 =========
 
 .. [1] Here **irregular** SEG-Y volume means the area covered by a SEG-Y file is not a rectangle but a polygon (meaning that some lines are missing some traces), or its inline/crossline intervals are not 1. 

README_ZH.md

@@ -7,6 +7,8 @@
   </tr>
 </table>
 
+## 中文版的README不是最新的, 只支持到1.1.5, 详情请参考英文版
+
 **此文件最后更新版本为 1.1.5**
 
 一个读写 `segy` 格式地震数据的 `python` 和 `c++` 工具。可以将 `segy` 格式文件读到内存或者直接转为二进制文件，也可以将一个 `numpy` 数据存储为`segy`格式的文件。
@@ -46,7 +48,6 @@ cigsegy.create_by_sharing_header('out.segy', 'header.segy', d, iline=, xline=, i
 - [用到的第三方依赖](#ThirdPart)
 - [两个在终端运行的可执行文件](#Executables)
 - [局限性](#Limitations)
-- [对比](#Comparison)
 - [感谢](#Acknowledge)
 
 <p id="Installation"></p>
@@ -360,45 +361,6 @@ segy.create('new_fx.segy', d)
 ### 局限性
 
 - 只测试过叠后数据
-- 只支持 4 字节的 IBM 浮点数和 4 字节的 IEEE 浮点数
-
-
-<p id="Comparison"></p>
-
-### 对比
-
-与`segysak`相比，我们的实现速度更快（`segysak`是纯`Python`实现）。
-
-在读取segy文件时，`cigsegy`比`segyio`稍慢，但差距很小。但是，`cigsegy`在创建`segy`文件时比`segyio`快。
-
-`segyio`假设文件是一个有序的三维数据集。它也支持仅由一系列道构成的文件（非严格模式），但在这种模式下，许多功能都被禁用，并会引发错误。然而，有许多segy文件是有序的，但其中缺少一些道。虽然这些文件很容易处理，
-但`segyio`不支持这些文件。`cigsegy`支持这些文件，只需使用相同的方法，例如`cigsegy.fromfile('miss.segy')`。此外，`cigsegy`还可以处理 inline 和 crossline 间隔不为1的文件。
-
-
-出于某些原因（保密要求、记录错误等），文件头可能损坏。如果您记得体积大小和采样格式（IBM为1，IEEE为5），
-`cigsegy` 也可以读取这些文件. 只需要使用
-```python
-d = cigsegy.fromfile_ignore_header('miss.segy', inline_size, crossline_size, time, dformat)
-```
-
-`segymat` 是在MATLAB中实现的，它的运行速度非常慢。
-
-`shape = (651, 951, 462) 1.3G`
-|mode|cigsegy|segyio|segysak|segymat|
-|---|---|---|---|---|
-|read|1.212s|0.944s|134.8s|151.99s|
-|create|3.01s|14.03s|-|-|
-
-
-
-对于 `cigsegy` and `segyio` 运行 `read` 3 次, 
-`segysak` 只运行一次, 
-`(1062, 2005, 2401) 20G` 
-|mode|cigsegy|segyio|segysak|segymat|
-|---|---|---|---|---|
-|read|45.6s+45.5s+45s|65s+20s+19s|612.45s|>1500s|
-|create|41.14s+43.35s|78.74s+82.74s|-|-|
-
 
 <p id="Acknowledge"></p>
 

build.sh

@@ -12,7 +12,7 @@ if [[ "$OSTYPE" == "linux-gnu"* ]]; then
   #   fi
   # done
 
-  cp -r /share/thridpart/fmt_2_24/* /usr/local/
+  cp -r /share/thridpart/fmt_8/* /usr/local/
   rm -rf /share/build
   mkdir /share/build
   rm -rf /share/wheels
@@ -23,7 +23,7 @@ if [[ "$OSTYPE" == "linux-gnu"* ]]; then
   do
     version="${cpyroot#/opt/_internal/cpython-}"
     version_min="${version%.*}"
-    if [ "$version_min" != "3.5" ] ; then
+    if [ "$version_min" != "3.13" ] ; then
       cpy=$cpyroot/bin/python3
       cpylib=$cpyroot/lib
       pypi=$cpyroot/bin/pip3
@@ -36,7 +36,7 @@ if [[ "$OSTYPE" == "linux-gnu"* ]]; then
       $pypi wheel .
       whl=`ls *.whl`
       prefix="${whl%linux_x86_64.whl}"
-      cp $whl /share/wheels/${prefix}manylinux_2_24_x86_64.whl
+      cp $whl /share/wheels/${prefix}manylinux2014_x86_64.whl
       # auditwheel repair $whl -w /share/wheelhouse/
       cd /share/build
       rm CMakeCache.txt
@@ -55,19 +55,26 @@ if [[ "$OSTYPE" == "linux-gnu"* ]]; then
   # done
 
 
-  rm -rf /share/thridpart/cigsegy/cigsegy*
-  rm -rf /share/thridpart/cigsegy/dist
-  rm -rf /share/thridpart/cigsegy/src
-  rm -rf /share/thridpart/cigsegy/python
-
+  rm -rf /share/thridpart/cigsegy
+  mkdir /share/thridpart/cigsegy
+
   cp -r /share/src /share/thridpart/cigsegy/
   cp -r /share/python /share/thridpart/cigsegy/
   cp -r /share/setup.py /share/thridpart/cigsegy/
-
+  cp -r /share/README.rst /share/thridpart/cigsegy/
+  cp -r /share/thridpart/fmt_8/include /share/thridpart/cigsegy/
+  cp /share/LICENSE /share/thridpart/cigsegy/
+
+  echo "include LICENSE  
+  recursive-include python *.pyi *.py *.cpp  
+  recursive-include src *.h *.hpp *.cpp  
+  recursive-include include *.h *.hpp" > /share/thridpart/cigsegy/MANIFEST.in
+
   sed -i "s/fmt_root = ''/fmt_root = '.'/" /share/thridpart/cigsegy/setup.py
-
+  sed -i "s/'numpy'/'numpy', 'pybind11'/g" /share/thridpart/cigsegy/setup.py
+
   cd /share/thridpart/cigsegy/
-  python=/opt/_internal/cpython-3.9.15/bin/python3
+  python=/opt/_internal/cpython-3.11.9/bin/python3
   ${python} setup.py sdist
   mv /share/thridpart/cigsegy/dist/*.tar.gz /share/wheels/
 

docs/changelog.rst

@@ -2,6 +2,19 @@
 Changelog
 #########
 
+v1.1.7
+--------
+
+- Refine the ``scan`` function to support more situations.
+- Add supports for dealing with more data sample formats, such as 4-byte, two's complement integer.
+- Add a new class ``SegyNP`` to simulate the segy file accessed as a numpy array.
+- Add functions: ``scan_unsorted3D`` and ``load_unsorted3D`` to support 3D unsorted data.
+- Remove the comparison part of the documents, as ``segysak`` has a large update.
+- ``use_guess`` in the functions like ``metaInfo`` has been deseperated.
+- Added more atomic operations, enabling finer control of SEG-Y files
+- And more ...
+
+
 v1.1.6
 -------
 

docs/core/SegyNP.rst

@@ -0,0 +1,45 @@
+SegyNP class
+###################
+
+This class can help you treat SEG-Y files as 3D/2D numpy arrays, without reading the whole file into memory.
+This means the reading process only occurs when you access the data, such as a part of data.
+
+
+3D array
+==========
+
+If the SEG-Y file is a 3D post-stack seismic file:
+
+.. code-block:: python
+
+    >>> from cigsegy import SegyNP
+    >>> d = SegyNP('3Dpoststack.sgy', iline=189, xline=193)
+    >>> d.shape # (ni, nx, nt), use as a numpy array, 3D geometry
+    >> sx = d[100] # the 100-th inline profile
+    >> sx = d[100:200] # return a 3D array with shape (100, nx, nt)
+    >> sx = d[:, 200, :] # the 200-th crossline profile
+    >> sx = d[:, :, 100] # the 100-th time slice, note, it may be slow if the file is large
+    >> sx.min(), sx.max() 
+    # get the min and max value, but they are evaluated from a part of data, 
+    # so they may not be the real min and max value
+    >> sx.trace_cout # get the number of traces for the file
+    >> sx.close() # close the file
+
+
+2D array
+==========
+
+If you don't want to create a 3D geometry, just treat the SEG-Y file as a collection of 
+1D traces, i.e., a 2D array, you can use the following code:
+
+.. code-block:: python
+
+    >>> from cigsegy import SegyNP
+    >>> d = SegyNP('2Dseismic.sgy', as_2d=True)
+    >>> d.shape # (trace_count, nt), use as a numpy array, collection of 1D traces
+    >> sx = d[100] # the 100-th trace
+    >> sx = d[100:200] # return a 2D array with shape (100, nt)
+    >> sx.min(), sx.max() 
+    # get the min and max value, but they are evaluated from a part of data, 
+    # so they may not be the real min and max value
+    >> sx.trace_cout # the number of traces for the file